History Recap / StargateAtlantisS05E02TheSeed

* TyrantTakesTheHelm: 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 is what ultimately convinces John to give their new boss a chance.

* RealLifeWritesThePlot: Woolsey replacing the original Atlantis Conference Room table with one from Earth. According to Joseph Mallozzi, the original table's distinct horseshoe shape made shooting in the cramped Conference Room set very difficult. They used Woolsey becoming the Expedition Leader as an in-story means of finally getting rid of it.

* TyrantTakesTheHelm: 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 andshowing vulnerability to Sheppard is what convinces John to give their new boss a chance.

* TyrantTakesTheHelm: 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, the crisis and Woolsey showing vulnerability to Sheppard is what convinces him to give their new boss a chance.

* TyrantTakesTheHelm: 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 grudge towards the IOA over how they treated Weir). However, the crisis and Woolsey showing vulnerability to Sheppard is what convinces him to give their new boss a chance.

* HoistByHerOwnPetard: 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). 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.

* NiceJobBreakingItHero: [[spoiler: 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 during ''The Prodigal.]]

* InSpiteOfaNail: 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).

* InSpiteOfNail: 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).

* HoistByHerOwnPetard. This is stated in-story by Sheppard to be the reason for Carter's removal: 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 was in early Season Four (Weir's presumed death, the near-destruction of Atlantis, the Asuran conflict). Now that those crises have been resolved during Carter's tenure, the IOA has used that 'Mission Accomplished' as an excuse to reassert full control of the Expedition.

* HoistByHerOwnPetard. This is stated in-story by Sheppard to be the reason for Carter's removal: She was ''too successful'' at her job. The IOA only grudgingly acquiesced to the appointment of a military commander rather than a civilian due due to the state of affairs at the beginning of Season Four (Weir's presumed death, the near-destruction of Atlantis, the Asuran conflict). Now that those crises have been resolved during Carter's tenure, the IOA has used that 'Mission Accomplished' as an excuse to reassert full control of the Expedition.

* VoiceOfTheLegion: Once the proto-hiveship infection develops enough, it starts to communicate with the Atlantis crew, using a monstrously-distorted version of Keller's voice. It retrospect, it doesn't sound that different from a Goa'uld.
* WasOnceAMan: Keller. Her situation invokes some serious FridgeHorror: apparently Wraith hiveships are created by infecting intelligent beings with a biological agent, which promply hijacks their brains and directs their bodies to build the structure of the ship. That means that every hiveship our heroes have faced was once some poor luckless human.

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 CombatTentacles.

* BaitAndSwitchTyrant: Woolsey actually turns out to be quite a competant leader.

-->'''Beckett:''' Remember the formula comes from Michael. So as far as we know it could...

* VoiceOfTheLegion: Once the proto-hiveship infection develops enough, it starts to communicate with the Atlantis crew, using a monstrously-distorted version of Keller's voice. It retrospect, it doesn't sound that different from a Goa'uld..

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 NaughtyTentacles.

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 NaughtyTentacles, and then covers her with his pistol just in case it doesn't work.

* NaughtyTentacles

* WasOnceAMan: Keller

* BaitAndSwitchUmbridge: Woolsey actually turns out to be quite a competant leader.

* CallBack: Several to [[Recap/StargateAtlanitsS02E08Conversion "Conversion"]], namely Beckett's hypothesis about the infected being able to sneak in safely and the following line: