The Prodigal

"The Prodigal" is the fourteenth episode of the fifth season of Stargate Atlantis.

Synopsis
Michael Kenmore has infiltrated Atlantis with an army of his Hybrids, and closes off Stargate Operations and the surrounded levels to prevent anyone from taking it back. His plan; take Teyla and her child to perfect his Hybrids, and to destroy the base when they're done. Meanwhile, Sheppard, McKay and a team try to take back the city before Michael leaves with what he wants.

Plot
In an ordinary night in Atlantis, Ronon Dex is in the Commander's office, seeing Richard Woolsey, who tells him that Ronon has not made a single mission report since he announced to everyone that they should since the fourth day he took command. He tells Ronon he knows he saw him there, when Ronon tells him that he doesn't remember being in the mandatory announcement. Anticipating that Ronon may not be good at writing, he gives Ronon a recording device, where from now on, he is to say out his mission reports, though he says he is not good at talking either.

Meanwhile, John Sheppard and Rodney McKay are racing remote controlled cars, seeing who is better. In the process, a passing Teyla Emmagan almost trips on one of them. She tells the men that she is walking her son, Torren John Emmagan to sleep, since this is the only way he could sleep. The men tell her that they will stop racing cars. However, as she leaves, they continue on racing. Teyla goes to her quarters, and hands Torren to a cradle to let him sleep. As McKay examines his car, the lights on their corridor turn off. Thinking it is just a power glitch, they radio the control room, but there is no reply. They try contacting other people, but gets no response either. The two walk over to a balcony, where they see that the entire city is blacked out. However, the lights from the control room are still on, which raises some questions.

Sheppard and McKay enter a section where other Atlantis Expedition members are gathering. Sheppard grabs a handful of flashlights, and walkie talkies, since radios are offline. Some of the Sheppard's men split up to cover more ground, when Radek Zelenka arrives, and informs them that everything is offline, they cannot connect the ZPM or Naquadah generators to any of the systems, they're completely dead. They plan to reboot the power in the main power room. Meanwhile, Teyla can't open her door, and tries to radio for help, not knowing everything is down. Eventually, the door opens, and Teyla wonders who it is. However, the two darkened figures raise their Wraith handblasters, and stuns Teyla.

Zelenka cannot reboot the power, and tells Sheppard and an exhausted McKay, who has to use the stairs because the transporters aren't operational. McKay believes that if the entire city is dead, an external power source of somekind is powering the control room. The two proceed to continue to near the control room. They eventually make it, while Zelenka works on the transporters. McKay and Sheppard notice that the door to the stairwell leading to the control room are sealed off. They believe someone has infiltrated the base. Zelenka calls McKay and tells him that he has initiated a temporary patch and rerouted it into his lab. McKay goes to his lab, while Sheppard and Major Evan Lorne and his team are planning to blow the doors open.

McKay and Zelenka, who are both in McKay's lab cannot access the control room. However, they do have access to the CCTV cameras, to give them a better understanding as to what is going on. Immediately, they find out that there is a Puddle Jumper in the embarkation area, and that the control room is being operated by non-familiar people. They see Teyla awakening in the office, where a familiar face walks in; Michael.

In a flashback, Woolsey finishes debriefing Ronon, when the Gate activates. They pick up Major Nelson's IDC. A Jumper arrives instead, and it initialises an energy field of somekind. Ronon suspects a trap, and urges everyone to run out. However, the field expands, stunning everyone. Michael and his squad of Hybrids begin working right away. The Hybrids close off all power and use their Jumper as their power source. Michael plans to bring Torren to perfect his Hybrid research, and then destroy the city, as retribution to what Atlantis has done to him. However, eventually he wants Teyla to join him, as he feels she is special to him. But when she refuses to come with him, he angrily tells her that he will get what he came for, and she will be killed.

Sheppard and Lorne plan to storm the control room, where Sheppard tells the team that if they have a shot at Michael, they must take, not risking to keep him alive. They blow the doors open with C-4, and climbs up the stairs to the control room. However, McKay picks up an energy reading, and tells the team to stop. Lorne is struck by a stun field of some sort. With that plan gone, they have to think of a new strategy.

Meanwhile, Ronon awakens in a room, full of personnel, who were stunned. Ronon tries to open the door to escape. However, he cannot do so. Eventually, Amelia Banks wakes up. Ronon tells her that someone has taken over Atlantis, and wants her to open the door. Banks manages to get the door open. However, the door is guarded by a Hybrid, which Ronon tries to fend off. However, the Hybrid eventually manages to get the upper hand, when Banks surprisingly fights him until Ronon is able to get a stunner and shoots him. Banks explains that she has learned kickboxing for five years. The rest of the imprisoned teams start to come round, where Ronon tells them they must arm themselves and take back the city.

Zelenka and McKay discover that the "stun bubble" (named by Zelenka) is made from Wraith stunner technology integrated with the cloak. They decide to destroy Michael's Jumper with a drone weapon. However, powering the control chair is out of the question, and the Jumper bay is out of reach. However, there are two Jumpers in the underwater bay. However, they're both not operational, so McKay has to fix them.

Ronon overhears Michael's plans to blow up the city, and they armed the self destruct. Ronon thinks of a new plan instead, and tells the team to return to the room. There, he charges up to the control room, stunning a couple of Hybrids, and encounters Michael. They engage in hand-to-hand combat. Teyla takes the opportunity to run with Torren, where she sees Woolsey, who guides her to safety. However, as they run down some stairs, Woolsey steps on the stun bubble, where he hurtles to the lower floor. Teyla is cornered, but uses the stun field to her advantage, as she pushes a Hybrid down, where he too is stunned. Ronon continues fighting with Michael, but despite having the upper hand, Michael catches him off guard, and Ronon falls down to the floor below, knocking him unconscious. Teyla tries to find a location to hide. However, with Hybrids after her, she is cornered. She eventually finds a hidden door and hides with her son.

McKay and Sheppard arrive at one of the Jumpers, where McKay learns that the Jumper can't fire drones. Sheppard plans on ramming Michael's Jumper, but there is another problem, the inertial dampeners are out, meaning Sheppard has to under go the on a tenth suicide mission. However, McKay has to finish fixing soon, as Michael activates the self-destruct to lure Teyla out of hiding. They have 10 minutes left. Michael talks to Teyla over the comm system, and tells her she has 10 minutes to show herself, or they will all die, including Torren. If she surrenders, he promises not to harm her in any way. Eventually Teyla talks back, telling him to deactivate the self destruct, then she'll surrender, so he can trust her.

McKay finds out that Zelenka can deactivate the Stargate shield. This means that if they can, Sheppard would be close enough to dial a random planet, so the unstable vortex could disable the Jumper, so they can retake the control room. Sheppard decides McKay should pilot the Jumper, so he can be a member in his strike team. McKay flies the Jumper to outside the control tower.

With two minutes left, Teyla urges Michael to deactivate the self-destruct. However, Michael's mood swings gets the better of him, and tells her that he has Torren's DNA to work with, so he plans to leave Atlantis, so it can be destroyed. Before they enter, Michael decides to get his prize, Ronon's head, and is about to cut it off, when Zelenka deactivates the Gate shield. McKay quickly dials a planet, where the unstable vortex destroys a good portion of Michael's ship, which deactivates the stun bubble and self destruct, and power to the entire city is restored.

Sheppard heads a strike team to the control room, where they kill all the Hybrids. Sheppard takes cover as Michael fires at him, but Sheppard is able to wound him, forcing him to flee. Sheppard follows Michael, who is heading to the Jumper bay to escape. Zelenka manages to close the roof, preventing his escape. With nowhere to go, Michael runs up a set of stairs, where he ends up at a dead end on the top of the tower. However, he is still able to surprise Sheppard, and almost throws him over. Sheppard gets back up and starts engaging Michael in hand-to-hand combat. Meanwhile, Teyla learn what Sheppard is doing, and hands Torren to Amelia.

Michael is quickly able to get the upper hand, and is about to beat Sheppard to death, when Teyla joins in on the fight. The two are able to push Michael over the edge, where he desperately holds on for his life. Struggling to get up, he begs Teyla to help him up. However, for a minute, Teyla gazes down on him, and eventually kicks both his hands off the ledge, where Michael falls hundreds of feet, to his death.

In the infirmary, Woolsey, who has sprained arm checks up on Ronon, who is recovering from his fall. He tells Ronon that his actions continues to amaze, and inspire him. As he leaves, Ronon tells Woolsey that he has finished a mission report on the Michael event. As Woolsey leaves, he listens to the digital recorder, where he hears Ronon say "Mission report. Michael invaded Atlantis, tried to blow it up. We stopped him. End of report."

McKay and Sheppard continue to race remote controlled cars, where they stumble into Teyla again, she tells them that Torren has actually slept through the whole ordeal, which he hasn't done since ever. She also says that even though Michael's dead, she knows that someone else has taken charge of his reign. But for now, they decide to have some time off, where she agrees to see the men race each other, where Sheppard cheats, by ignoring the countdown.

Notable Quotes

 * Ronon's recorded "mission report": "Mission report: Michael invaded Atlantis, tried to blow it up, we stopped him. End of report."

Background notes

 * Jennifer Keller does not appear in the episode.
 * This episode marks the death of Michael.
 * Atlantis Expedition countries shown: Belgium, Canada, India, Spain and United States of America
 * Goof; Near the beginning of the episode, after McKay and Sheppard attempt to climb up to the control room, McKay is seen with sweat dripping from his hair and has a sweat stained shirt. Shortly thereafter in his lab, his shirt is completely dry and his hair is dry and styled.
 * Goof; Teyla said that Torren slept through the whole ordeal. Yet when she was hidding him in the wall (in the corridor) he's awake.
 * Woolsey at the end of the episode says "Listen to what the doctor says." This is something his actor Robert Picardo used to say when he played the Emergency Medical Hologram in Star Trek:Voyager.

Production

 * The working titles of this episode included "The Red Shirt Diaries", "First Day", and then just "Prodigal", until "The" was added.