It's nearing the end of a mundane day on Atlantis — Sheppard and McKay are racing RC cars, Teyla is trying to get baby Torren to go to sleep, and Woolsey is struggling to get Ronon to actually fill out mission reports. Suddenly, the city's power goes out. After failing to contact the control room, Sheppard and McKay manage to get ahold of the security feeds — only to discover that the culprit is Michael, not nearly as dead as previously expected. He's come to take Teyla's son to further his research into controlling his Hybrids, and he plans to blow up Atlantis on the way out. Complicating things is an area-denial device he's set up — a force field that instantly stuns anyone who attempts to cross it, blocking access to the control tower.
Tropes:
- Attack the Injury: After being disarmed by Michael, Sheppard is having trouble in a fistfight against the super-strong hybrid. Sheppard manages to regain the advantage, though, by hitting the bullet wound he'd inflicted to Michael shortly before.
- Back for the Dead: Michael appears again after being presumed dead in his last appearance, and this time is more permanently dispatched.
- Bookends:
- Sheppard and McCay racing the RC cars in the hallway, only for Teyla to interrupt them carrying her baby.
- Michael dies in Atlantis, where he was "born".
- Brick Joke: Ronon's mission report.Ronon: Mission report. Michael invaded Atlantis, tried to blow it up. We stopped him. End of report.
- Call-Back: The Underwater Jumper Bay from Season Three's "The Return, Part 2" (and the flooded Jumpers) ends up playing a crucial role in the Expedition's counterattack against Michael.
- Continuity Nod: When Rodney protests Sheppard's plan to crash a Jumper into the Control Tower, Sheppard reminds him that they've crashed Jumpers into the Tower before.
- Disney Villain Death: Michael.
- Evil Is Petty: Even with the city's Self Destruct activated, Michael delays his escape... because he just can't pass up the opportunity to stick it to Ronan (who he's despised since "Michael") one last time. This delay gives Radek and Rodney the crucial seconds they need to re-activate the Control Room's Stargate and destroy Michael's Puddle Jumper.
- Grand Finale: Of the Michael storyline that began late Season Two.
- Hand Stomp: A rare heroic version where Teyla kicks Michael's hands off of the precipice.
- Hypocritical Humor: Rodney mocks Zelenka's "Stun Bubble" description of Michael's siege weapon... only to accidentally call it the "Stun Bubble" moments later. Rodney's annoyed, mid-sentence realization and Radek's look of smug vindication are what really sell it.
- Inertial Dampening: A plot point. This is why Sheppard's planned attack run on the Control Tower initially looks like a guaranteed suicide run. The damaged Jumper can't fire Drones, necessitating a ramming attack...except Rodney can't repair its inertial dampers in enough time. So, Sheppard will have to hit the Tower at full speed and the force of impact will realistically crush him like a bug. Fortunately, the plan becomes moot once Radek figures out how to lower the Gate's shield.
- Insistent Terminology: McKay absolutely refuses to call Michael's area-of-effect stun device a "stun bubble". It's a force field, thank you very much.
- Joker Immunity: Michael's inability to stay dead no matter how many times the Expedition seemingly kills him rivals Apophis over on SG-1. Rodney even lampshades it.McKay: [Michael's] like a cockroach, you know? Every time you try to step on him, he just skitters away.
- Killed Off for Real: Michael finally dies for good (and fittingly in the very place where he was created).
- Mama Bear: Teyla goes into full-on Mama Bear mode on Michael. When will villains learn not to mess with the Action Girl's children?
- Never My Fault:
- Michael still blames everything that's happened to him on the Atlantis crew. And to be fair, he may have a point about some of it. But when Teyla points out that their actions against him had nothing to do with his decision to unleash a horrifically virulent plague on millions of innocent humans, Michael angrily continues to claim that he had no choice.
- Zigzagged with Rodney when Sheppard realizes that even 2 years later, Rodney still hasn't repaired the Jumpers from the Underwater Bay. Rodney admits it was his responsibility...but Rodney being Rodney, he also tries to shirk some of said responsibility by saying he was getting to it 'eventually'. In his defense, the Expedition's had a lot on its plate with since "The Return, Part 2".
- Nice Job Breaking It, Hero:
- Woolsey's refusal to continue the search for Michael back in "The Seed" and his dismissal of the team's fears that Michael stole the Puddle jumper in "Search and Rescue" come back to bite him and the Expedition in the ass hard here.
- Rodney's failure to repair the drowned Jumpers from "The Return" complicates Shepard's plan to get past the Stun Bubble.
- Playing with Syringes: Michael, as usual; he's still trying to get his hands on Teyla's baby so he can use his DNA to perfect his army of Hybrids.
- Running Gag: A Black Comedy example when it looks like Sheppard's about to do another suicide run. Rodney and John even lampshade they've lost track of just how many times Sheppard's had to pursue this option at this point in the show's run.
- Suicide Attack: In the climax, it looks like Sheppard's going to have to crash a Puddle jumper into the Control Tower at the cost of his own life.
- Villain Ball: Twice, on Michael's part. He obtains Teyla and Torren very quickly, and could easily make good his escape by simply leaving immediately. Instead, he delays leaving until he's sure they can destroy Atlantis — and he tries to do this using the self-destruct, which requires a lengthy process to crack the encryption protecting that system first. This takes enough time that Ronon wakes up and tries to attack Michael in the control room, creating a distraction that lets Teyla run and hide with Torren. At this point Michael could still win by leaving right away — as he says himself, he's taken enough samples to clone the baby and complete his project. But he's decided that he wants Teyla to come with him, so he instead sets the self-destruct to flush her out and waits for her to come to him. Eventually it becomes clear that's not happening, so he tells Teyla it's too late and starts to leave... seconds before Sheppard and McKay destroy his ship, which shuts down his "stun bubble", deactivates the self-destruct, and cuts off his escape in one stroke.
