- The rules are there for a reason, Colonel. If I can't trust them, then...I'm not sure I can do this job.— Richard Woolsey
Richard Woolsey of the IOA assumes command of Atlantis, to everybody's consternation. The first thing he does is to call a progress meeting, to see what everybody's been up to in the three weeks he was on the Daedalus. They haven't found any trace of Michael, but are still looking, since it seems likely that he stole the cloaked jumper and escaped when his hiveship blew up. The hybridized Athosians are making good progress in returning to humanity, with the help of Beckett's retrovirus and Michael's notes. And, with everything quited down for the moment, Keller has been devoting all of her time to figuring out how to save the still-in-stastis Dr. Beckett, but she has reached the limit of what she can get from Michael's notes.
Woolsey opts to shelve the search for Michael, to cries of distress from the others. He makes himself even less popular by telling Keller that it's a waste of time to continue working on the Beckett problem. It's not as bad as it seems though—if she's reached the end of what she can do in the lab, she has to either wake him up or shelve the problem. They decide to wake him up.
Dr. Keller's treatment seems to work—Beckett is alive and functioning at least, but is still suffering a lot of damage to all of his various organs. Woolsey will be sending him back to Earth for long term hospitalization at the next dial-out. Dr. Keller, however, has started having some problems herself, beginning with waking up with her hand covered in slime. She washes off the slime and doesn't tell anybody… and the next day she doesn't report in for work.
McKay and Teyla break into her room and find her unconscious and covered with a plant-like growth. Fortunately, Dr. Beckett is up and about, and has seen something similar while he was Michael's prisoner. Dr. Keller is in the process of turning into a hive ship, due to a pathogen she picked up digging Sheppard and the others out of Michael's lab. Sheppard, Ronon, and McKay (and presumably Lorne and Carter) are also infected, and Beckett orders them quarantined. Unfortunately he's got to head back to Earth in about an hour - but he begs Woolsey to let him stay on until the emergency has been dealt with.
And it's shaping up to be a bit more of an emergency than they'd originally though. The plant hiveship thing is seeking out power to help grow—and when they cut the power to Keller's isolation ward it heads right for the main power conduit and the ZPM. Zelenka and Teyla go in to see how far it has gotten and whether they can halt it's progress, but it senses Zelenka is a threat and attacks him.
Zelenka escapes with just a concussion, but it's clear they need another plan. Beckett hypothesizes that the entity might not consider someone else who was infected to be a threat. Better yet, he's managed to create a drug that he thinks will separate Keller from the tentacle vine things. He tests it on Sheppard, and when Sheppard manages not to die he sends Ronon in to administer it to Keller. Things go great until Ronon encounters a blocked hallway and has to blast his way through—at which point Hive-Keller recognizes him as a threat and ties him up with Combat Tentacles.
It's about this time that Sheppard wakes up, fully cured. Rather than sending in McKay as the only other infected-but-asymptomatic person on the base, Sheppard takes a jumper, the antidote, and a pistol, and ploughs his way right into Keller's ward. He injects her with the antidote, but not before he gets a little impaled by the aforementioned tentacles and then covers her with his pistol just in case it doesn't work.
Fortunately, it does, and Keller ends up recovering faster than Sheppard does. Oh, and Ronon has a crushed larynx, but it's unlikely anyone will notice the difference. They finally send Beckett back to Earth, and the IOA decides not to immediately fire Woolsey for commiting over half a dozen breaches of protocol in his first three days on the job.
Tropes:
- Bait-and-Switch Tyrant: Woolsey actually turns out to be quite a competent leader.
- Body Horror
- Bothering by the Book: Despite the fact that Woolsey was installed by the IOA specifically because of his penchant for this, the first crisis on his watch forces him to defy it. When Sheppard lampshades this, Woolsey tells him "Don't get used to it." After the crisis has passed, Woolsey claims "The rules are there for a reason."Woolsey: If I can't trust them, then I'm not sure I can do this job.
- Call-Back: Several to "Conversion", namely Beckett's hypothesis about the infected being able to sneak in safely and the following line:Beckett: Remember the formula comes from Michael. So as far as we know it could…Sheppard: Turn me into a bug? Been there, done that.
- Converse with the Unconscious: According to Keller, McKay made a secret habit of going in and talking to Dr. Beckett in his stasis pod.
- Hoist by Her Own Petard: This is stated in-story by Sheppard to be the reason for Carter's removal from the Expedition: She was too successful at her job. The IOA only grudgingly acquiesced to the appointment of a military commander rather than a civilian due to how bad the situation in Pegasus had become in early Season Four (Weir's presumed death, the near-destruction of Atlantis, the Asuran conflict, etc.). Now that those crises have been resolved during Carter's tenure, the IOA have wasted no time using 'Mission Accomplished!' as an excuse to reassert full control of the Expedition and put one of their own in the big chair.
- Impaled with Extreme Prejudice: Sheppard.
- In Spite of a Nail: Even with the changes to the timeline, Keller observes that elements of the possible future John saw in "The Last Man" are still comng to pass (i.e. Woolsey taking over the Expedition). Sheppard doesn't reveal (though he nearly spills the beans) that Rodney and Keller hooked up in that timeline; he's clearly wondering if 'his' Rodney and Keller will follow that same path (which ultimately they will).
- Nice Job Breaking It, Hero: Woolsey ignores the circumstantial evidence from the theft of the stolen Puddle Jumper during "Search and Rescue" and dismisses the team's fears that Michael may very well have escaped his flagship's destruction. This will come back to bite him and the rest of the Expedition in the ass later in the Season.
- Spotlight-Stealing Squad: Sheppard strays into this territory, robbing Ronon of the spotlight twice in the same episode.
- Tyrant Takes the Helm: Initially played straight-ish when Woolsey arrives at Atlantis. While technically just a bureaucrat, nobody on the Expedition especially likes Woolsey from his previous visits, or by how Carter was ousted (and that's before getting into Sheppard's preexisting grudge towards the IOA over how they treated Weir). However, Woolsey's handling of the crisis and showing vulnerability to Sheppard afterwards is what ultimately convinces John to give their new boss a chance.
- Voice of the Legion: Once the proto-hiveship infection develops enough, it starts to communicate with the Atlantis crew, using a distorted version of Keller's voice. It retrospect, it doesn't sound that different from a Goa'uld.
- Was Once a Man: Keller. Her situation invokes some serious
Fridge Horror: apparently Wraith hiveships are created by infecting intelligent beings with a biological agent, which, like a virus, hijacks their brains and uses their bodies' resources to build the structure of the ship. That means that every hiveship our heroes have faced was once some poor luckless human.
