Atl_Season2Info

Season Two

This is not an Episode Guide and as such the information provided isn't necessarily in chronological order or set in context. In other words, you will need to know the general plot for much of this to make sense.

In some cases I have quoted extensively from the transcripts (especially so in the Science section). This is usually when I feel the character(s) say it better than I could, and paraphrasing might lose some of the details.

I have four sections: Timing, Personal Character Information, General Information, and Techno-Babble and Science.

PLEASE NOTE that I have not completed all of Season Two.

Seige, Part 3	The Hive
Intruder	Epiphany
Runner	Critical Mass
Duet	Michael
Condemned	Inferno
Trinity	Allies
Instinct	Links
Conversion

Siege, Part 3

Timing:

The episode picks up straight from the end of the previous one.
After the 2 hive ships have been destroyed and the scene in which Beckett explains that Ford’s body has become dependent on the Wraith enzyme (before Ford regains consciousness), McKay and Zelenka say that the deep space sensors have finally come back online and that there are 12 hive ships heading for Atlantis, which will arrive in 36 hours.
When the second wave of hive ships start their bombardment, McKay says that the ZPM will be depleted within days. Caldwell says they can have the Daedalus repaired in 24 hours, “but I think the next engagement's gonna have the same result.”

Personal Character Information:

Everett is fed on by a Wraith, and although he survives is badly aged. He is being sent back to Earth with the first batch of wounded. He says he understands why Sheppard killed Sumner and wished he had been there for him as well.
Ford is addicted to the Wraith enzyme and in a fit of paranoia escapes from the infirmary, steals a jumper and gates out of Atlantis.
First time we see the Daedalus and Colonel Stephen Caldwell.

General Information:

The authentication code Caldwell uses to get Sheppard to de-cloak is Alpha Charlie One.
When the gate tech picks up another ship and is asked if it is a hive ship he says, “Negative. Reading IFF.”
The weapons officer on the Daedalus is Dave Kleinman, a Second Lieutenant (GateWorld omnipedia). The pilot (at least for this episode) is Cooper (Abydos transcripts). Hermiod is the Asgard assigned to the ship.
The Daedalus lands on the east pier – please note, on screen it looks like it lands on the water, which I find confusing; there may be a metal platform under the water, otherwise the ship must be capable of floating on the surface.

Techno-Babble and Science:

The Daedalus is equipped with Asgard technology, including beaming tech. It is armed with rail guns as well as Mark-8 nuclear warheads. They use the beaming technology to deploy the warheads inside the Wraith ships (against Hermiod’s wishes) and destroy the 2 hive ships over Atlantis. When they later take the fight to the Wraith, they are able to destroy another 2 ships before the Wraith employ countermeasures, stopping them from beaming onboard their ships. This is when a Wraith cruiser attempts to dock with them; important to note for next episode.
When the darts start a suicide run at the city Zelenka says that the approach is ballistic and, “Their impact velocity will be in excess of ten thousand kilometres an hour. No part of the city can withstand that.”
The Wraith that attempts to feed on Ford dies after giving him a dose of the enzyme;
“We still have no idea how it works, but during the Wraith feeding process, the victim is injected with a special enzyme. It strengthens the human body temporarily and insures that the heart continues to beat…So the victim doesn't die immediately. The feeding process is so traumatic. Without the special enzyme, we'd shut down far sooner than they'd like… In most cases the enzyme is released slowly into the blood stream throughout the feeding process. I can only ascertain that the Wraith died quite suddenly, and that Lieutenant Ford's system became flooded with it... The problem is now the enzyme is breaking down in his system. Eventually, there'll be none left… I'm quite certain it will kill him. It's possible his body has become dependent on the enzyme to function” (Beckett) They harvest more enzyme from the dead Wraith so that they can wean Ford off it and, “Sneak his body chemistry back to normal incrementally” (Beckett).
After Ford leaves the infirmary without permission and nearly throttles Beckett, he is sedated. “It's starting to affect his brain chemistry…We need to be more aggressive. Wean him off it quicker than I expected to. It’ll be painful and arduous. I think it may be the only option.” (Beckett)
”The Wraith's faster than light travel is not as efficient as the Asgard hyperdrive aboard the Daedalus. [Clicks on a remote and the screen behind him changes.] Not only are they slower, they need to travel in a series of jumps. So if my calculations are correct, they'll make one last stop here... [points to a spot on the map] ...fifty light years away, before they make the final jump to Atlantis.” (McKay)
McKay admits that they don’t know how the Ancients sunk the city.
“The puddlejumpers are equipped with cloaking technology, which renders them invisible to the naked eye, and to Wraith scans. If we just simply remove one of the cloak generators from the puddlejumper…” (Zelenka) “... I wouldn't say simply, but yes, by interfacing a Jumper's stealth mode generator with the city shield, we should be able to render the city invisible… we fake a self-destruct. Have the Daedalus beam a nuke right above the city's shield and then detonate it. While their sensors are blinded, we cloak the city…” (McKay). “What about hard radiation?” (Caldwell) “I should be able to calculate with reasonable accuracy how long to wait before we switch over to the cloak.” (McKay) “…what about the displacement issues?” (Zelenka) “…Its coplanar emulation? That is the easy part…(the hard part)... the cloak for all intents and purposes will replace the shield. Which means that we'll be completely unprotected once the cloak's activated” (McKay). Caldwell believe the Daedalus could break through the lines and escape if it all goes wrong, so they put as many nonessential personnel as possible onboard. Teyla will contact the Wraith when they are closer, “…if I can convince them, that we intend to destroy Atlantis rather than allow it to taken. Just before the explosion occurs... if the Wraith believe that we intend to destroy the city, the last thing they'll want to do is to help us do it” and so the bombardment will stop and that will tell them the Wraith have bought it.

Intruder

Timing:

Caldwell states that it has been at least two months since the ship encountered the Wraith.
Weir states at beginning of the episode that it’s been almost a month since Sheppard’s promotion.
It takes eighteen days on the Daedalus to get from Earth to Atlantis.
Caldwell states that they will be back in Atlantis in less than 2 days.

Personal Character Information:

Sheppard has been promoted to Lieutenant Colonel; he says there were many people who thought he’d never make it past Captain.
Elizabeth and John both admit to feeling odd returning to Earth. Elizabeth is frustrated by how long it is taking to get back to Atlantis.
Sheppard can’t help but stare at Hermiod, he thinks it’s weird they’re working with an alien and appears uncomfortable with the Asgard’s nakedness. McKay, on the other hand, seems perfectly fine around Hermiod, treating him like he treats everyone.
Simon Wallis eventually admits to Weir that he is seeing someone else.
Beckett believes that all of the candidates are more qualified than he is (Weir calls him her chief surgeon, and reassures him that no one is more qualified than him). He hands her a rather long ‘short’ list to make the final decisions on who to employ.
Ford’s has a cousin called Lara. As he didn’t have any brothers or sisters they became very close. His grandparents are both still alive.
McKay feels cramped inside the cockpit of the F-302 (which he has never been in before) and worries about how much air supply there is – he appears to be a touch claustrophobic.
McKay worries they are getting too close to the sun, “See, the thing is I have very fair skin. I can get burned very easily”. At end of episode his face is red, his nose is peeling and he asks Beckett for more moisturizer.
Teyla says there has been no word on Ford from her off world contacts.
Zelenka is excited about the many discoveries they have been making since gaining a ZPM.

General Information:

“McKay says we're already at the edge of the Pegasus Galaxy...” (Sheppard at beginning of the episode to Weir).
The International Committee approved “a significant increase in personnel and resources for the Atlantis mission” (Landry). Weir says that they can accommodate more people now that they have a ZPM. She has brought back all her senior staff as she thinks “…it's only fair that they participate in the selection process of the new personnel in their respective departments”.
Weir backs down Landry and the other military present when they try to replace Sheppard as military commander on Atlantis; this is what leads to his promotion.
Lindstrom and McKay go to check the power distributions to try and work out what caused the power spike. Lindstrom is onto something when there is a coolant leak and he ends up in the air lock, which opens. This is when Sheppard suggests the security cameras are being used to monitor the investigation.
The Daedalus went through a full decontamination sweep when it reached Earth.
The Daedalus fighter bay has a shield.

Techno-Babble and Science:

The Virus:

“I think it's possible. That Doctor Monroe's death might not have been an accident... I checked the power distribution logs against the time code on the security camera. There was an unexplained spike, but it happened a whole thirty seconds after the camera went out… So that means the malfunction in the door and the camera were not caused by the same problem. Major Sheppard was right. That's too much of a coincidence… and there is something else. It looks like Doctor Monroe was in the process of enabling certain computer security protocols. They're designed to isolate and shut down corrupted programming… I know this sounds crazy. But there is definitely more going on here then random malfunctions.” (McKay – note stumble over Sheppard’s rank).

Hermiod discovers a virus in “one of the navigational computers. There is evidence of it in communications and some of the propulsion systems as well… It appears to be rewriting itself as it grows. It is unlike any human engineered program I have ever encountered.” McKay runs it through a translation program and discovers that it is Wraith.

“It was probably downloaded during our last little encounter…in all likelihood, it was transmitted in a compressed format. It took a while to unfold to... spread to the point where it could adversely affect our systems. I think it probably happened during the return flight to Earth. Since then it's been dormant waiting for some kind of a trigger… Possibly the fact that we're once again in proximity to Wraith territory. I think it was ultimately designed to take control of the navigational system: Fly the ship right to 'em.” (McKay) Weir realises that with the Daedalus the Wraith will have access to intergalactic hyperdrive technology as well as the navigational data they need to find Earth.

When asked who killed Munroe and Lindstrom McKay replies, “…it's the virus. Look, it's an AI, an artificial intelligence. It can think for itself adapt itself to new situations... It knew that Lindstrom and Monroe were gonna expose it, so it got rid of them.” When asked if it could take over the ship, he replies, “…not entirely. You have to remember there are hundreds of individual computers onboard. A lot of them are interconnected so we can tend to think of them as one big machine, but that's not really the case. There are dozens of back ups and redundancies and some systems, like life support, are deliberately isolated…. That was the good news. The bad news is some of the more complex systems like navigation and propulsion require certain amount of interconnectivity to function properly. In all likelihood, the virus has spread so far through those systems that to isolate it would make the ship impossible to fly. Till we figure out how to get rid of it, we're stuck here.”

The virus sends out a distress beacon that they can’t shut down. “This is what I mean by adapting itself to new situations. It doesn't have enough control yet to fly us to the Wraith, so instead, it's calling the Wraith to us. And right now we are sitting ducks.” (McKay). Sheppard flies a F-302 and shoots out the transmitter. The virus has uploaded itself to the F-302, which navigational software is compatible with the sublight systems which are infected, and it flies away from the ship. They manage to beam him back.

The attempt a shut down and reboot of the ship’s computer systems to get rid of the virus. The virus returns after they engage sublight engines and heads them towards the nearest sun. “…a more precise calculation of our heading shows that we will not collide with the star, but rather make a close approach, near its coronasphere. The ship will survive, but the radiation will kill everyone on board.” (Hermiod). The virus knows that they would destroy the ship rather than let it fall into Wraith hands and so intends to get rid of the crew. McKay realises that the virus uploaded itself onto the F-302’s and hid there until the shut down had been completed. Sheppard and he have to physically remove the memory storage modules and then do another shut down. In the end they have to destroy the rogue F-302 that Sheppard had used to destroy the transmitter before a third and final shut down gets rid of the virus.

The beaming tech was not designed to “beam from one point to another point inside the ship” (McKay), however it works fine to get them into the hangar bay after the virus shuts them out.
At the sort of speeds that the F-302’s go, as well as the sort of manoeuvres that Sheppard is making, even with inertial dampeners whoever is onboard will still feel movement.

Runner

Timing:

About one week since Intruder, according to McKay
When Sheppard, McKay etc return to look for Ford it is dark but McKay says that “the sun will be up in two hours, forty-three minutes, and... ten seconds”.

Personal Character Information:

First appearance of Major Lorne in Atlantis (previously appeared in ‘Enemy Mine, SG1’s Season 7).
First, and so far only, appearance of Dr Parrish, botanist.
“You know, when they told me I'd be travelling to another galaxy, visiting a strange new worlds, defending humanity against unimaginable alien threats, this is just not what I pictured” (Lorne – not happy to be babysitting a scientist).
McKay worries about the UV levels and radiation on the planet and has brought 100 SPF sunscreen (with a “simulated tropical aroma of coco butter”) that is waterproof and he has made himself. Later, “…by my calculations, we've been exposed to three hundred and twenty seven millisieverts since the sun came up. It may not sound like much to you, but I've been keep a running tally of my lifetime exposure to radiation. X-rays, cell phones, plane rides, that whole unfortunate Genii nuclear reactor thing. And…last week we flew dangerously close to the corona of the sun. As it is I may have to forgo reproducing”.
McKay says that Sheppard is wearing Aqua Velva.
We meet Specialist Ronon Dex, ex-military and runner. He knows the stargate as the Ring of the Ancestors. Ford killed the Wraith that was hunting Ronon. “I was captured during a culling of my planet. Was taken to a ship. The Wraith started to feed on me. Something made him stop… They operated on me. Put some sort of a tracking device in my back and released me… I hunted them back. I've been running ever since.” He has been running for 7 years, not being able to stop for fear of bringing the Wraith down on people. “One time I accidentally came across a planet with a village near the ring… Stayed. One night and ate a meal for a change. Left right away the next day. Didn't matter. I later heard. The whole village...” (interrupted before he finishes the sentence). He has Wraith feeding scars on his chest, and scars on his back from when he tried to remove the tracker himself, though “…most of it’s from two different doctors”. He is from Sateda, which he discovers was destroyed by the Wraith some time ago.

General Information:

Major Lorne refers to the dead Wraith as a ‘sucker’; it has been dead no more than a day and was KIA (Killed In Action).
Kaufman and Reed are mentioned by Lorne as being back on the planet and covering the gate. Then, when they split up into groups, it is Sheppard and Teyla, Lorne and McKay, Kaufman and Villick, Reed and Sherman. However, later on it is Kaufman and Reed together when they come across McKay, and Ford stuns them.
The planet’s designation is P3M-736 and McKay says that “…the UV index there during the day is something like... a thousand”.
As far as I know, this is the first time the term ‘life signs detector’ is actually used in an episode.
When Lorne and McKay first encounter someone, Lorne radios Sheppard to say that they are 2 klicks south of the gate. Teyla and Sheppard are also following someone, but are too far away for it to be the same person.
“We haven't heard from them since. 26:30 Atlantis standard time” (Lorne reporting Teyla and Sheppard’s disappearance). “I know the life signs detector doesn't work there, Major. But can you use the Jumper to search from the air?” (Weir) “No, ma'am, the foliage is far too dense for that” (Lorne). Weir sends another team to assist. McKay requests she also sends through the 4 class one radiation suits from the med lab storage rooms.
McKay shoots Ford in the shoulder and looks pretty upset at doing so, before fear takes over and he runs (ending up caught in a leg hole trap). Ford looks pretty shocked too, before anger takes over and he goes after McKay intending to kill him.
3 Wraith darts come through the gate after Beckett has finished the surgery on Ronon and McKay is running from Ford.

Techno-Babble and Science:

“We could be saving Earth. Right here. Right now… Through a greater understanding of the long term effects of severe ozone depletion on plant life. You may not want to admit it, but it's a real danger…I don't think there's much chance that any animal survive long term effects of exposure to the sunlight on this planet… It's the fact this vegetation is thriving... Somehow it's managed to persist despite there should be extremely destructive ionizing radiation. [looks at a plant on a tree.] Oh, would you look at that?! Now what is a Williamsonia sewardiana doing here?” (Parrish)
“Doctor Parrish believes that the indigenous plant life retains enough residual radio activity absorbed during the daylight to... um... well... to screw up our sensors” (McKay on why the life signs detector isn’t working).
”…the cloud covering will depreciate a small percentage of UV rays, but ninety-five percent of deadly is still deadly” (McKay) “Doctor Parrish said that a day or two of exposure wasn't going to kill us” (Lorne) “Oh, yes, and Doctor Parrish has a PhD in what? Right, Botany” (McKay).
The tracker in Ronon is located “…in the soft tissue next to the second thoracic vertebrae” and means that Beckett will need to cut “…very close to your spinal column…” (Beckett).

Duet

Timing:
No information given.

Personal Character Information:

It is Zelenka’s first time off world and he is very jumpy.
“And do you have a degree in physics, hmm? Well, what about mechanical engineering?” (McKay to Cadman – so he has at least 2 degrees). On his wall in his quarters there are a lot of certificates; one is from Northeastern, a university in Boston, US, and is a doctorate, though I can’t quite make out what in. I have been reliably informed that some of the certificates on McKay’s wall are made out to ‘Rodney Ingram McKay’. Unfortunately my screen capture isn’t up to capturing these details.
Lieutenant Cadman was one of the “…new batch that came aboard the Daedalus…” (Beckett).
McKay’s cat photo in his quarters is of a white cat, not the tabby we see in Rising. There is another photo on his desk, but I can't make out what is pictured. His quarters have a balcony with plants on it (can be seen through the window that the head of his bed is against).
McKay has a prescription mattress for his back.
When Ronon asks Teyla why she joined these people she answers, “My people are strong and proud. But Atlantis is the best hope for us all. I suspect you see it too or you would have already left”.
Cadman, when she thinks they might not survive the de-materialisation and re- materialisation process, hijacks McKay’s body for the last time and kisses Beckett, much to McKay’s horror (and Beckett’s none too pleased either).
McKay is snoring slightly before he wakes up at the end of the episode.
Beckett gives Cadman’s hand a squeeze before leaving them alone; we know later that the two of them get together (see Epiphany, Critical Mass).

General Information:

Cadman knows about McKay’s date with Katie Brown, a botanist, from the girl’s poker night.
This is the episode that McKay refers to Zelenka as “Dr. Fumbles McStupid”.
“She's been able to access the part of your brain that creates speech and controls hearing. So why not movement” Heightmeyer to McKay, she goes on to suggest that if he lets go Cadman might be able to control his body, which she does. (Note, some think that Heightmeyer’s statement is an error, but I interpret it that Cadman is able to speak to McKay and therefore in that sense has already accessed speech and hearing.)
Sheppard persuades Weir to let Ronon join the team despite her reservations.

Techno-Babble and Science:

Wraith beam:

“…it's very complex. This interface controls the machine that de-materialises people, stores their information, and then re-materialises them again when commanded to” (Zelenka) “From what we can tell, the re-materialiser is storing two life signs” (Beckett) “…but there is only enough power in the Dart's energy cell to successfully re-materialised one of them. Power to the re-materialiser has been severed and emergency back up power has completely gone down... You have to decide which one we are going to have to beam out” (Zelenka). They can’t distinguish between the life signs, and so Sheppard chooses one at random; it’s McKay, who falls down unconscious.

“…the good news is we were able to stabilize her life sign signature. Now is just the question of getting the machine online again… the bad news. The machine uses a very specialized transformer to convert raw power into highly stable, very specific stream of power. Now the transformer is crucial in operating the machine safely and uh... it's been damaged… We're working on a reverse engineering one” (Zelenka).

“Now I assume you've tried to run one of our own generators with this thing” (McKay) “It's not as simple as that…We think it is having it's having in interface with the Wraith machine in real time the power fluctuations are huge. If we over shoot just a little, we'd screw up” (Zelenka) “...we can maybe write up an interface program that can take care of all this...” (McKay). He is going on to say something about using a naquadah generator when Cadman interrupts him.

“I was able to get the generator to run on a buffer low which restricts the dart into taking only the part that it needs without overloading” (Zelenka). However, the trial doesn’t work as the mice are re-materialised dead and burnt.

“…the gate de-materialises you as you step into it. Sending your information to the next gate, so you re-materialise on the other side... So if we can take on of the crystal control modules from the gate and interface it with the dart. We should be able to build a stable system” (McKay). McKay’s idea works in the simulations, but Zelenka wants to test it out on mice first. McKay says he might not have time for that. Fortunately the process works and McKay and Cadman are successfully re-materialised as themselves, falling unconscious.

McKay suffers a seizure; “From what we can tell, the constant fighting over the dominance of your brain is having a deleterious affect of its lower functions: heart rate, respiration, organ function... I'm not sure how long you can go on like this… These misfires will only increase in frequency and severity with time..” (Beckett). One of them has to let release control, let go completely, which would cause whichever one who let go to “…disappear. I know they would 'cause I can already feel it happening to me. It's getting harder to be in here. It's taking more of an effort” (Cadman). Cadman offers to let go, McKay is not happy about it.
“This is a P-90. It's compact and lightweight. Incredibly sturdy, full…[DEX starts shooting at the target in the centre.]…That's good. [puts down the P-90] All right, this is a 9-mm, semiautomatic...” (Sheppard).

Condemned

Timing:

When they reach the downed jumper after escaping from Torrell, McKay says he needs about ten minutes to get the DHD working. When Torrell’s men return, he shouts to Sheppard that it will be two minutes.

Personal Character Information:

Ronon tastes the unknown stew, and later he is seen putting food in his pockets while in the apartment they are given in the Olesian city.
“I prefer lethal injection. Although I do have a certain fondness for the electric chair. Call me a romantic” (McKay about corporal punishment, said in a sardonic tone of voice – when Teyla asks if all of their countries kill violent criminals, he answers some of them and Sheppard asks that they not get into this).
Ronon is seen stashing food in his pockets during the above scene.
“Margaret Thatcher wasn't creepy. Okay... maybe a little. She actually resembled an aunt of mine. Same hair style, facial structure, only my aunt was much taller and remarkable hirsute. The oddest thing, she had to shave twice a day” (McKay).
“I think I chipped a tooth. Did I chip a tooth? Cause I believe… I am a high risk of endocarditis” (McKay’s hypochondria flares up after the crash and is ignored by the team).

General Information:

The vessel that saves the team’s life at the beginning of the episode is the Olesian security vessel Boros.
The island with the ‘ancestral ring’ or stargate is a penal colony and has been for hundreds of years. Despite assurances otherwise, it is no longer only violent criminals sent there, but anyone who commits a crime is in danger. By the end of the episode, people are being arrested apparently randomly to boost the prison colony’s population.
Some Prisoner Psych 101 on McKay, take it as you will:

“You strike me as the type of man, who despite being weak and cowardly on the outside, harbours a strength of character. He doesn't even know he has... See the way to motivate a man like you, Mister McKay. Is not to threaten your life. It's to threaten the lives of your friends…Fix the ship. Otherwise they start dying one after another. Till you change your mind, or until they are all dead. I don't care.” (Torrell).

“I know your type. You whine and you complain and you see to it that your every task is viewed as some impossible achievement, so that when you do succeed. Your gargantuan efforts are viewed all the more heroic” (Torrell) “That maybe true in some cases, but this is not one of them. You are asking me to do the impossible” (McKay).

McKay has an idea (see techno-babble section) that might not work and only admits it later (after Sheppard says he is a terrible liar).

“I must admit. I still find it intriguing to watch you eat actual food” (Magistrate to Wraith) “Our lineage may have diverged, but there are those of us who retain an appreciation for finer things. And although it may provide a moments pleasure, it does not sustain. [stands up] This arrangement I have with you and your predecessors have served both of us well. While others of my kind have been force to sleep between cullings, I have enjoyed a steady stream of human for my consumption and the taste of their defiance is sweet. You, in return had been allowed to live in peace...But throughout the galaxy, Hives continue to wake in far greater number than are sustainable. And with the hunger it is most pressing… why is it that there are even fewer inhabitants on the island? Others of my kind would have destroyed your entire planet, but I am more civilized than that… Still, there are interests which must be served. There are many Wraith who hunger, and I have promised to provide for them. The decision you are now faced with is on whom shall we feed?” (Wraith).

Techno-Babble and Science:

“Our scientists have recently attained success in the enrichment of a fissionable yet non-radioactive material to be used in generating power for the city” (Magistrate) “Fissionable yet non-radioactive. That...even possible? What kind of material is it?” (McKay) “It's an ore. Extracted from a mineral found on our planet. It's quite volatile and yields great promise” (Magistrate). Needless to say, McKay is very interested in seeing this.
“…the main power distribution conduits been damaged. In fact that means it cuts off all the power to the primary systems: drive pods, cockpit controls, DHD…” (McKay, and he can’t fix it without a replacement).
“I won't actually be able to fix the ship and fly out of here, but I might be able to cobble together enough power from secondary systems routed to the DHD. That way we can dial the gate and leave on foot…” (McKay). The power, though, is intermittent.

Trinity

Timing:
No information given.

Personal Character Information:

“…I can eat frozen dinners without even thawing them…” (McKay)
Ronon admits about Atlantis that “... this place has everything I could want” but sometimes he needs to go “Anywhere else”. Teyla also knows this feeling.
Elizabeth says about Rodney, “Confidence is not something that Doctor McKay is in any short supply of…I know Rodney McKay, and there are times when I have to protect him from himself.”
“…And to bring this up now, when I'm just about to do this smacks of nothing but professional jealousy.” (McKay to Zelenka when he has been told the experiment is too dangerous and won’t listen).
The relationship between McKay and Sheppard is damaged as a result of the events in this episode. McKay asks Sheppard to trust him, says he won’t let him down and then almost gets them both killed. “I already apologized to Elizabeth and Radek and I thanked Colonel Caldwell for caring enough to spy on the experiment from orbit. Sent him a nice little E-mail actually. But I saved you till last because... I would…hate that recent events might have permanently dimmed your faith in my abilities or your trust. At the very least, I hope I can earn that back.” (McKay) “That may take a while…But I'm sure you can do it. If you really want to give it a try.” (Sheppard).

General Information:

“Well give me Optican, Collins, and... uh Zelenka if he's over the stomach flu.” (McKay to Weir, organising the team to take back to Doranda).
“The Belkans possess a particular disease resistant strain of flax seed, which would double the yield of our crops on the mainland. In exchange I intend to offer Athosian man power to aid in their harvest.” (Teyla to Ronon, explaining her trade visit to Belkan).
Sateda survivors:

Ronon discovers that he is not the only survivor from Sateda. We meet Solen Sentia, who is telling a tale to his friends “…Now I was alone. I was low on ammo, but I managed to take out the three Wraith guards and gain access to that ship.” Ronon calls him a liar, but when Solen sees who it is he just grins. “There were two Wraith guarding that cruiser, and he wasn't alone” Ronon explains. They served in the same regimen.

About three hundred people survived by hiding in the ‘west bunkers’ and left Sateda as they was nothing left to salvage. Some went to Manaria (the people here double-crossed Atlantis in The Storm, Season One), some to Belkan.

Ronon’s task master, Kell, is alive. “…and his family. They settled on Belsa. Run this big trading operation over there… he comes around every now and then to trade weapons with the Belkans. He's got his own private army now...” (Solen) and then to Teyla’s question of whether he is a friend of Ronon’s, “he's more like kin. He was Ronon's task master during his military training. There is no closer bond.” (Solen)

“Kell commanded several infantry divisions in Sateda, and when the Wraith came, he order thousands to their deaths, just to save himself. He was a traitor and a coward...” (Ronon explaining to Teyla why he killed Kell.) “I understand. In your place I might have done the same. But believe me when I tell you that the others would not. We must not speak of this when we return to Atlantis, and if you ever use my friendship in such a way again. I will not be so understanding.” (Teyla’s response).

“Harry K. Daghlian…He was a scientist worked on the Manhattan Project at Los Alamos. He was only twenty-six years old. Accidentally irradiated himself while performing a critical mass experiment on two half spheres of plutonium. Took him a month to die. While his body was slowly shutting down from radiation poisoning...He tried until his last breath to understand what had happened to him. So that others could learn from the tragedy. So that his work, his death wouldn't be rendered meaningless. Now, have you considered what would have happened if they just shut the project down after that?…Collins's death is a pointless waste of life unless something comes of this and...” (McKay to Sheppard).

Techno-Babble and Science:

Project Arcturus:

“From what we can tell, it's a ground base version of the satellite weapon we used to destroy that Hive.” (Sheppard) “With one major exception: firepower. I mean that single outpost was responsible for destroying an entire Wraith fleet.” (McKay)

When Sheppard asks if they have tried turning on the weapon yet McKay says “…The problem is that there is no direct link between it and the main power control systems, which among other things, have led us to theorize that it's an ancillary power supply for the weapons systems.” Zelenka adds later “…it's much more than that.” - “Well, the sticking point is that there is no tie between the power generator and the primary capacitor.” (McKay) “…meaning they would have to channel the power directly into the weapon.” (Zelenka) “Means they can fire multiple bursts without having to store more power for the firing sequence.” (Sheppard – to McKay’s surprise – works out what their techno-babble means!) McKay then adds “It seems the Ancient were experimenting with high energy physics on a level that we've never seen before.”

“It's the ultimate power source. Something that would make Zero Point Modules seem like alkaline batteries in comparison…It's called Project Arcturus. From what we can tell, its ultimate goal was to render ZedPMs obsolete…The Zero Point Module is an artificially created region of subspace time. It's kind of like a miniature universe in a bottle.” (McKay) “It's extracts vacuum energy from its artificial region of subspace time until it reaches maximum entropy…Project Arcturus was attempting to extract vacuum energy from our own space time. Making it potential as powerful as a scope of the universe itself.” (Zelenka) “…but extracting zero point energy from our own universe is... Well, it's definitely trickier.” (McKay) “…because we actually have to live in our own universe. It presents a whole range of problems.” (Zelenka).

They fire up the weapon: “I'm picking up some other power fluctuations. Chamber temperatures holding steady...” (Zelenka) “Everything is fine. The containment bottle was designed to automatically compensate for any sudden changes in energy output.” (McKay) “This never happened in the simulations.” (Zelenka) McKay orders Collins to try and “…boost more power to the field manually.” They prepare to test fire and the levels go into the red, and Collins is killed. They try to shut it down but “the interface is not responding!” (Zelenka) McKay says to switch to back ups, but the levels are going off the scale. “I have given the command to shut down, but something is creating an overload.” (McKay) Then it stabilizes and the generator goes offline. Sheppard asked what happened. “Obviously, there was a surge of some kind.” (McKay)

“We're still analyzing data from the test. All we know for certain was there was a massive power surge, which in turn caused the containment field to expand asymmetrically in the direction of the command access tube. As to why...” (Zelenka about what went wrong). Caldwell suggest Collins made an error. “No. Collins knew the systems just as well as any of us. He wouldn't have made that kind of mistake.” (McKay).

“The Ancients had it wrong. Our mistake was using their equation…I just did the calculations again myself. I did them three times, just to be sure. And I am positive that the problem is in the automatic containment protocol… I'm proposing that we adjust the field strength manually… we don't operate the generator at anywhere as near its potential...Even operating at fifty percent, it will still generate the power of a dozen ZedPMs.” (McKay) When asked what the worst case scenario might be by Sheppard, McKay responds, “We tear a hole in the fabric of the universe...look, the risks are nothing compared to the potential benefits…”

Zelenka raises concerns, “I've been doing calculations of my own and I believe that the very act of trying to contain vacuum energy from our own space time creates an environment where the laws of physics cease to apply…As power output increases, new and exotic particles are continuously created and destroyed inside the containment chamber. Interacting with each other and with the field itself, eventually particles are created that can not be predicted in this space... And they breach the containment field as hard radiation…You can not predict something that is inherently unpredictable…I believe if the overload is allowed to continue the weapon acts as a sort of release valve to prevent catastrophic containment failure. The Ancients barely managed to shut it down and they lost their lives in the process.” Weir adds that they believe the weapon killed the Dorandans not the Wraith.

McKay can’t control the overload and isn’t able to shut it down. They leave in the jumper but have to zigzag to avoid the weapon’s fire. The jumper won’t take more than one direct hit and they can’t fly out of range of the explosion as, “…When this thing blows its going to take out three quarters of the solar system…” (McKay). Fortunately the Daedalus is there to help them out.

McKay sends “an encoded data burst directly from the outpost to the secure network in my lab, while the gate was active” on their way back from Doranda. The technician receives the data and transfers it.
”Officially, my report will indicate that Doctor Collins died due to radiation exposure. Causing severe burns to well over ninety percent of his body... To be honest I have no idea what sort of radiation it was. I've never seen or heard of cellular decay this massive. Not when exposure only lasted mere seconds.” (Beckett)

Instinct

Timing:
(Section Not Complete)

John says iratus bug incident was ‘a year ago’

Conversion

Timing:
(Section Not Complete)

At end, John says a couple of weeks cooped up in infirmary, and then says ‘the past few weeks’.

The Hive

Timing:
(Section Not Complete)

Planet is ‘only a few days away’ at start of this episode – reaches planet by end of episode.

Epiphany

Personal Character Information:
(Section Not Complete)

Rodney says he still can’t fly the jumper in a straight line (!).

Critical Mass

Timing:
(Section Not Complete)

Takes place over at least a day to a day and a half (re: Wraith cruisers comment from Rodney)

Michael

Personal Character Information:
(Section Not Complete)

This is the episode that Rodney says that blue jello is his favourite.

Inferno

Timing:
(Section Not Complete)

The Hive ship is three weeks out when detected in this episode.

Allies

Timing:
(Section Not Complete)

Over two years ago, Wraith were awoken (i.e. Rising).

Season 1 Season 3

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