Allies

"Allies" is the twentieth episode of the second season of Stargate: Atlantis.

Synopsis
A Hive Ship arrives to Atlantis and makes contact with them. It is Michael Kenmore, who proposes the expedition to supply them with the Iratus bug retrovirus to turn enemy Wraith into Humans, to serve as an alternative food supply.

Previously on Stargate: Atlantis
The Atlantis expedition uses Dr. Carson Beckett's Iratus bug retrovirus to turn a Wraith into a Human. With the Wraith's memory gone, he is told his name is Lt. Michael Kenmore but he quickly discovers the truth. He escapes and takes Teyla Emmagan hostage. Lt. Colonel John Sheppard is able to rescue Teyla but Michael returns to the Wraith with the knowledge that Atlantis still exists. Sheppard and his team discover another Aurora-class battleship called the Orion on the planet Taranis. The Long range sensors detect a Hive ship heading for Atlantis.

Plot
A Wraith Hive ship is approaching Atlantis. While the Daedalus and the Orion wait in some distance from the city, Atlantis itself is cloaked. Suddenly the city is contacted and it turns out that it is Michael Kenmore, the Wraith that they attempted to turn into a human. Though initially wary of his intentions, interest is sparked when Michael claims that the Wraith are being divided by a civil war and says that they want to use Dr. Carson Beckett's Iratus bug retrovirus to turn their rivals into humans to feed upon. In return, Michael promises to turn over valuable technical information about their weapons and defenses. They start by sending a possible method to use their transport technology again to beam Nuclear warheads inside the Hive ships.

The leadership of Atlantis discuss what to do and finally agree to provide assistance, although Teyla Emmagan is a bit reluctant. Afterwards Michael, the Wraith Queen and her chief scientist come to Atlantis. Once Beckett reveals that he has found a way to transform the retrovirus into an aerosol gas, the Wraith insist that he help devise a plan to disperse it inside their enemy's ships. Later the gas is tested on a captured Wraith and it works. This results in the queen feeding on the victim. However when the Wraith try to use the gas on an enemy ship, they fail and when the Daedalus tries to help it is damaged. To find a way to better dispatch the virus, the Wraith give Dr. Rodney McKay a computer file, a treasure trove of information about Wraith technology that he needs to complete the job.

Yet, as is soon discovered, this unusual partnership is too good to be true. While Ronon Dex still harbors deep suspicions about Michael, others on the Atlantis team hope that the alliance will buy time and help protect humans on other worlds from attack. Yet, once the assault on the enemy ship is underway, Dr. Elizabeth Weir and her team discover that they have played into a trap. Following the crash of Dr. Radek Zelenka's computer terminal and an attack on the Daedalus by both Wraith ships, it becomes clear that the alliance was just an elaborate ruse. Finally, with McKay and Ronon taken hostage aboard the Hive ship, Zelenka uncovers a worm-like computer virus that was uploaded into the Atlantis computers, giving the Wraith access to information that will make possible a devastating attack against Earth.

Notable Quotes
McKay: They didn't need you on the Daedalus?

Hermiod: Colonel Caldwell believed my time was better spent disabling their jamming code.

McKay: Huh! So, they can fly that ship without you.

Hermiod: Yes. But apparently you cannot run these tests without me.

McKay: I'm sure I would have been fine.

Hermiod: I am not as sure.

Sheppard: How's it coming?

Zelenka: Ah. Oh, it's, it's phenomenal. It's, it's like being handed a Wraith encyclopedia. It's hard to know where to start.

Sheppard: When I was a kid and I got my first encyclopedia, I started with the letter "S".

Zelenka: Yes, well, while I'm sure that Wraith sexuality is interesting, we've decided to split into two teams.

(the Wraith touches McKay's shoulder, Ronon attacks the Wraith)

McKay: Ronon, are you crazy?! Do you wanna get us killed?!

Ronon: (to the Wraith) You don't touch him.

McKay: He was guiding me down the hall, not sucking the life out of my shoulder! (to the Wraith) We are sorry. (to Ronon) Say you're sorry!

Wraith: That will not be necessary. He was protecting his superior. I would have done the same.

Ronon: He's not my superior.

McKay: Certainly not in... every sense.

Hive Queen: Getting to this location without arousing suspicion will be very difficult.

Weir: Sure it will be, but we can't really help you with that.

McKay: Although the Colonel and I have come up with a way to test that theory. Step one: we find another enemy hive and jump to a location just out of its sensor range.

Sheppard: Step two: the Daedalus takes position in close proximity to your hive, essentially merging with your scan patterns, rendering it practically invisible to the enemy sensors.

McKay: Step three: using sublight systems, our ships approach the target hive for... whatever reason; I'm sure you can come with something.

Sheppard: Step four: now that the Daedalus can use its beaming technology again...

McKay: which would be thanks to... (pointing to himself)

Sheppard: Anyway... once we get in range, we can beam the canister into the CO2 chamber and boom! One hive ship de-Wraithified.

McKay: Hmm. I should be on that hive when we do this.

Weir: Excuse me?!

Sheppard: Really?

McKay: I know it's uncharacteristically brave, but I've hacked a lot of their systems under the guise of repairing them. I've convinced them that I should be there to supervise their systems if anything goes wrong.

Weir: And they agreed to this?

McKay: Yes. Plus, now we can freely beam stuff on and off their ships ... I've written a program that will immediately beam me out of there the second I activate this emergency transponder.

Goofs

 * As the armed guards escorted the Wraith party through the corridors of Atlantis, all of their uniform patches, including those of the guards lining the corridors as well, were on the wrong sides, placing the Atlantis patch on the left arm and their flag on the right. This was due to the footage being flipped horizontally, as the padded shoulder strap of the guard's body armor (which is usually on the right shoulder/breast) was also on the wrong side.