First Contact

"First Contact" is the tenth episode and the mid-season finale of the fifth season of Stargate Atlantis.

Synopsis
Daniel Jackson arrives in Atlantis to investigate a hidden lab left behind by the rogue Ancient scientist Janus. Their discovery has attracted the attention of a mysterious group of aliens, who infiltrate the city. Meanwhile, "Todd" and a delegation arrive on the Daedalus to bring forward Keller's gene therapy.

Previously on Stargate Atlantis
Jennifer Keller and Sheppard's team make proposal to "Todd"; Keller has found a gene therapy from Michael's database that should allow the Wraith not to feed on Humans again. The Atlantis expedition has been made aware of an Ancient scientist named Janus, who kept performing unauthorised experiments, against the Ancient Council's wishes. Despite a number of times they order him to stop, he carries on with the experiments.

Plot
Doctor Rodney McKay and Lieutenant Colonel John Sheppard walks down a corridor to the Atlantis Gate Room. On the way, McKay complains that they shouldn't just go to the Gate Room everytime an important visitor arrives to Atlantis, since he is in the middle of work. They meet with Richard Woolsey in the Gate Room. The Daedalus arrives and beams down their guest, Dr. Daniel Jackson of SG-1. Woolsey welcomes him to Atlantis, where Jackson greets Sheppard, and an annoyed McKay.

He travels to Atlantis when his research suggests that the rebellious Ancient scientist named Janus may have hidden a secret lab somewhere within the city. Hoping to find it, and possibly a significant portion of his unauthorized research, Jackson enlists Dr. McKay's help to find the rumored laboratory.

Meanwhile, Woolsey plans to go to the Daedalus on a delegation with the Wraith to eliminate their need to feed. Since Woolsey has to go, protocol states that Sheppard must remain to lead the city, since he is the second-in-command. Jennifer Keller gets ready for packing supplies for her next mission. Ronon Dex offers to help and come with her, since her next mission involves the proposal with "Todd" a few missions ago, and he feels his presence can help due to several Wraith coming to the ship. Keller accepts the help, and pass both McKay and Jackson on the way. McKay later realizes that Ronon is with her, which makes McKay uneasy.

In a certain room, they both found an obscure log entry from one of Janus' assistants, stating that he was going to see Janus when he took a corner to a hallway, and when he came to see him, Janus mysteriously disappeared. They find the isolated hallway, which shows signs of flood damage, since the Expedition emptied it during the first year of their arrival, and never gave it a second thought. They find three mysterious slits, belonging to certain lights. They wonder where the lights are. They check the CCTV archive from before the hallway was emptied. They then trace back the three lights in a storage room, and them placed them on the slits back in the hallway.

Jackson notices that when touching the lights, they give off separate tones, believing it to be some kind of code. After some trial and error, which at first, doesn't succeed, McKay cracks the puzzle; touching them quickly, in sequence causes a series of harmonic pulses, which opens up the cloaked lab, by magnetically resonating a hidden door from solid to a state which can be walked through. They both enter the lab, and start investigating. However, inadvertently, a subspace transmitter activates. Meanwhile, on some ice-covered planet, in another Ancient lab, an obscure figure informs the rest of the group that they must leave to the origin of the signal.

Woolsey prepares a speech for the arrival of "Todd" and his Wraith, but discovers that when the Wraith arrive, they want the work to be completed as quickly as possible, despite "Todd's" skepticism. He also confessed that even if the drug does work, the Wraith might never go through with it. However, things do progress without incident as they worked together.

After nearly 24 hours, both McKay and Jackson are still at it in the lab. At the same time, a hyperspace window opens just above the ocean, a few hundred miles away from Atlantis, heading towards the city. The technicians notices this, and they find no IFF signal. They call for Sheppard, who tells them to launch the Puddle Jumpers and to activate the city's shield, since it is closing in. However, the mysterious ship manages to zoom right through the shields as if it isn't there. The ship hovers above one of the piers, where a section of the ship opens, with three figures descending down to one of the levels.

The mysterious aliens with battle armour erect a circular platform. Sheppard, Teyla Emmagan and confronts them and tells them to stop. However, they all stand on the platform, which cuts through the floors, leading to the same corridor right next to Janus' lab. As the strike teams rush down, Sheppard warns McKay and Jackson, and tells them to leave immediately. However, the aliens stuns them both, takes the signaling device and takes them back to the platform. Sheppard's strike team intercept one of the aliens, who activates a shield, rendering projectiles to harmlessly bounce off the shield. Sheppard's team sees two of the aliens with an unconscious Jackson and McKay lift off back to the ship, while the team finally brings down the remaining alien with enough firepower, depleting the shield and killing it.

A while later, Both Jackson and McKay wake up and finds that they are in a brig of some kind. They both try to figure out what happened, they both realise that there must've been a subspace transmitter that activated when they found and entered the lab, they both attempt to find a way to try and escape, but there was little time, as the ship arrives on the ice-covered planet.

Dr. Radek Zelenka is called into the hallway to examine the dead alien. The alien was indeed killed. They took it to the infirmary, where he is to examine the body. However, when he looks for whatever was inside the suit, Zelenka deduces that an EM field could render an Ancient scanner useless. He tries to cut into the suit, but barely leaves a mark before the saw's blade dulls out. He gets a bigger blade and cut into the neck, which is weaker than the rest. He manages to cut through it, but as this happens, Sheppard notices a flashing light, flashing and beeping faster. The team quickly evacuates, just before the suit blows up, which wipes out any chance on identifying the alien race.

McKay and Jackson enter a lab with an Ancient design. They both realize that it must be another one of Janus' labs. The aliens tell the scientist to activate a device. After doing some research in the computer terminals located in the room, Dr. McKay realizes that it is a very advanced piece of Ancient technology, the "end game machine", which could ultimately stop the Wraith once and for all. The device is meant to disrupt the exact subspace frequencies associated with Wraith hyperdrive systems, effectively causing any Wraith ship that attempts to enter a hyperspace window to be destroyed. Apparently the technology had a serious unforeseeable side effect, so Janus abandoned the research and the project. After Jackson and McKay try to explain all this to the Aliens, they are given an ultimatum; either they set up and activate the device, or Dr. Jackson will be killed. Dr. McKay quickly acquiesces to this request and the alien leaves them temporarily.

Zelenka thinks that he has found a way to track Jackson and McKay, but has to use a new form of math to find them, since he can backtrack where the other end of the transmission in. He thinks he has found out where they are, M6H-987. The problem is that the planet has no Stargate, meaning it is off the grid. They are out of communications range from the Daedalus, so they have to plan something else.

Jackson realizes that the aliens are possibly using the suit to protect themselves, and they must be hiding their true identities. McKay works on activating the device, and after an unknown amount of time, reactivates the device, in spite of both their wishes to the contrary. He then discovers what the side affect of the device is. They attempt to warn the aliens, since the side affect is very serious, but were stunned before they could warn them.

At roughly the same time, a ship in "Todd's" fleet hails the Daedalus, and "Todd" speaks with them privately. After inquiry from Mr. Woolsey and Colonel Steven Caldwell, "Todd" informs them two of his ships must depart for the moment, since a rival hive is attacking one of the Wraith outposts. They see the cruisers depart and entering their hyperspace windows. However, everyone witnesses that both Wraith cruisers are destroyed, once they enter hyperspace.

Suspecting an ambush, an angered "Todd" accused them of obtaining the "Attero device". He secretively pulls two energy rods from his coat sleeves and puts them together, creating an energy pulse that knocks everyone on the bridge unconscious. "Todd" assumes control of the Daedalus and starts to transport his other soldiers and assistants onboard. Ronon, walking the halls of one of the upper decks, sees the Wraith soldiers beam aboard and taking cover. He sees Dr. Keller and insists that they head to the ship armory, since the ship is under attack from the Wraith. However, this may be difficult, since "Todd" manages to lock down the ship, limiting the movements of every other Human on-board.

Back on Atlantis, Sheppard and his team are ready to contact the Daedalus by dialing the Stargate to M5R-179. However, after Chuck dials the Gate, it begins to go critical. They have seconds until the Gate will detonate, which will result in an explosion equivalent to a dozen nuclear bombs. Sheppard orders the city's shield to encompass the Gate. The Gate explodes, causing a blinding flash. Zelenka works on strengthening the shield, since the longer the shield holds, the smaller the explosion will be if it collapses. However, the shield emitters are overloading, so Sheppard evacuates everyone from the control tower. Only Sheppard and Zelenka remain. The shield is severely weakening. Seconds later, a fairly big explosion rocks the central control tower.

To be continued...

Notable quotes
Jackson: It's a puzzle. I think we need to activate these in a specific order.

McKay: You mean, like a three digit code? D'you know how easy that'd be to break?! There's only six variations!

Jackson: Well, maybe we need to activate them a number of times in a specific order. I don't suppose you recognise any of these three notes?

McKay: What, do you mean, like, does it remind me of Janus' favourite Brian Eno track?! No, no such luck.

"Todd" arrives onboard the Daedalus

Woolsey: Thank you for coming.

"Todd": Thank you for having us.

Woolsey: (clears his throat) Today is an historic day. Robert Grosseteste once said...

"Todd": I would like to get started as soon as possible.

Woolsey: Y-yes, of course. But I wanted to recognise...

"Todd": I have my doubts that your plan will be effective... so shall we drop these unfounded pleasantries and get to work?

Caldwell: Robert who?

Woolsey: (sighing) Never mind.

Jackson: Is everything a competition with you?

McKay: I'm not sure what you're talking about.

Jackson: I just found you a secret lab full of really cool Ancient stuff. I kind of think that should score me some points here.

Jackson: I've spent the majority of my professional life being ridiculed for my theories, most of which turned out to be correct, by the way. I'm kind of used to it, Rodney.

McKay: Doesn't that bother you? I mean, there's no vindication, no recognition, no credit.

Jackson: Well, I could say the same thing about you. The discoveries you've made, you probably could have won the Nobel Prize five times over by now.

McKay: It's too true. So, I guess none of us signed up to get famous, huh?

Jackson: No, we did it for the money.

McKay: Ha ha ha, Good one!

(McKay pauses for the moment and slowly looks to Jackson)

McKay: You don't get paid more than me do you?

(Jackson rolls his eye) McKay: You DO?

Jackson: Look, given the right amount of time, it's possible we could get the device to function safely, but we'd have to contact our people and bring in a much larger science team. See, I'm not that kind of scientist... and what my friend...

Alien: (interrupts and points to McKay) Get the device operational within one hour, or I will kill him. Do you understand?

McKay: (quickly) I understand, yes.

Todd: One of our facilities is under attack by a rival Hive. Our two support ships must depart for battle. My Hive will remain here; continue the work with Doctor Keller.

Woolsey: I'm glad to hear that.

(Both Todd and Caldwell turn and stare at him)

Woolsey: Oh, not the "under attack" part. That's unfortunate, of course. I-I just meant ...never mind.

Background notes

 * Teyla Emmagan announces the "Previously on Stargate Atlantis" in the beginning of the episode.
 * The SG-1 theme is briefly heard in the first few moments after the opening credits of this episode.


 * This episode shares its name with a Star Trek movie.


 * Tok'ra crates can be seen in Janus's secret outpost

Production

 * Michael Shanks guest stars as Daniel Jackson.