The episode begins and Gen. Bressler lets Tom and the 2nd Mass go. He explains he's been waiting for Manchester to come to his senses and let them go on the offensive, but since he's not, he's declaring martial law. Tom won't go along with it, so Bressler orders them locked back up. But before they can go back in their cells, there's a signal for an outer perimeter breech. They then charge upstairs to find skitters in the common area, led by Red Eye. Bressler's ready to shoot when Ben pops out from among the rebels. Bressler still won't give the order to stand down so members of the 2nd Mass stand in front of the skitters, in a sign of solidarity.
Finally, he relents. Later, Guards warily march Red Eye and Ben into Manchester's office. Ben speaks for him, with his spikes glowing. "Captain Weaver, I'm not sure you realize the prize you had when you captured the overlord last week," he explains. That overlord was in charge of military operations for the eastern US. Red Eye says it was a mistake to let him live. He explains the overlords are so smart; they don't use computers they keep everything in their heads. If that overlord had been killed, the alien efforts would have been thrown into chaos. Red Eye explains they have intel on when that overlord will be vulnerable again. The aliens are building a machine and the overlord will be there in three days to inspect it.
The rebels need the human's help because they can't approach undetected. Ben leaves with the rebels. Bressler doesn't believe it and shoots the mission down. He orders Tom and Weaver locked up again but Weaver suggests he let the 2nd Mass go on the mission. Bressler agrees. When they leave, Bressler orders Clemons to take out all the rebel skitters overnight. Outside the compound, Hal goes looking for Ben. He apologizes for what happened with Karen. Ben tells him he thinks he's found a place he belongs. Hal thinks he belongs with his family, but Ben's mind is made up. Back in Charleston, Anne and Lourdes pack up medical supplies when Anne has to break to barf. Tom doesn't know she's pregnant yet. She'll tell him after this mission. Up in his office, Manchester is indignant that he's under house arrest.
Tom is telling him again that they have to go fight when Ben comes in bleeding. His camp was attacked. At the camp, there are dead skitters and harnessed kids everywhere. Bressler asks if he saw who did it; Clemons collects evidence of his own attack. Bressler cancels Tom's mission. Ben in the meanwhile, tells his dad the mission is about more than taking out the overlord; the machine they're building is very dangerous. Red Eye had more evidence than he was willing to share with Bressler. Tom and Weaver tell Bressler they're going and he puts up a show of objecting, but is secretly pleased when they go forward. Dai, Maggie, Anthony and Weaver on the other hand pack up weapons. Tom's daughter Jean wants to go, but he tells her she should stay in Charleston and help rebuild.
She's worried about losing him but he assures her he'll be fine. Ben in the meanwhile, draws up plans of the machine layout from memory. Tector rejoins the Berserkers, explaining he shot Lyle in the arm so Clemons wouldn't kill him. Pope accepts him back. Tom on the other hand tells Matt that he wants him to stay behind and keep Lourdes safe. Anne joins Tom. The 2nd Mass rolls out. On site, they poke through the cramped underground tunnels. Ben leads Weaver and the rest to a wall, where he expects the chamber to be on the other side. He tells Tom he can feel that the overlord is there. Dai and Anthony blow the wall. The small 2nd Mass goes through into a giant cavernous space with an equally large glowing machine in the middle of the chamber. They all wonder how long until the aliens show up.
They split up to lay out C4 around the machine of the towering machine. It's pointing up at the sky. Ben says it wasn't meant for humans. Ben's harness starts to glow and skitters rush in. One skewers Dai before anyone can react. More skitters rush in and they try to fight them off but the skitters quickly grab each of them. Karen comes in. It is shown that, all the humans are strung up by their hands at the base of the machine. The overlord shows up. Karen tells them they're all going to die, but first they're going to talk. Karen wields the torture stick she used before on Tom, and then turns it to Hal, but she kisses him instead. He then passes out. She then zaps Weaver. She in the end moves on to Anne and is about to zap her when she puts her head on Anne's stomach instead.
She tells Tom that Anne's pregnant with his child. Karen's about to zap Anne when Tom says, he'll tell them anything they want to know. Just then, a group of rebel skitters bust in. The alien restraints that were holding the humans go slack and they fall to the ground, free. The rebels attack as Red Eye jumps on the overlord. They fight, but eventually, the overlord gets the upper hand and slices him with a talon. Tom meanwhile grabs the zapping torture stick and races at the overlord. He swipes his legs out from under him, knocking him to the ground. He stabs him repeatedly with the stick. Karen tells Tom it's not over and he'll never win, then she scampers up the walls and gets away. Ben on the other hand tends to Red Eye, who is beyond help.
He gives Ben a message and takes Tom's hand, telling him to keep the fight going. Tom and Ben carry the unconscious Hal out of there. They regroup and leave. Safely outside, they blow the machine. They return to Charleston, carting Dai's body and Hal. "Mission accomplished, sir," Weaver reports to Bressler. They come home to a hero's welcome. Tom gets a big hug from his daughter. Matt asks Ben if he's staying. Tom starts to explain that Ben has important work to do, but Ben says he is. In sick bay, Anne says there's technically nothing wrong with Hal. They just have to wait and see what happens. Tom tells Anne he's happy she's pregnant, but she wonders how fair it is to bring a child into this world. He tells her they have to if there's ever going to be a future.
Hal wakes up from his hospital bed with no one else around. He goes to the mirror and a small bug crawls out of his eye and into his ear. He smiles. Tom on the other hand visits Manchester. Bressler as it turns out has agreed to restore civil rule if Manchester gives up the office of majority leader, which he's fine with. Manchester thinks Tom would be perfect for the job. Tom is flattered, but he tells Manchester that he and Weaver have already agreed that Charleston is not the place for the 2nd Mass. They have to keep fighting.
Outside, Tom tells Weaver the sooner they get out of Charleston, the better. Suddenly, the walls start to quake. Everyone runs outside and looks up to the sky, which is full of lightning and dark clouds. There's a high pitched whine and suddenly blue lights start falling from the sky; they're pod ships. One lands directly in front of the 2nd Mass and opens up. A new kind of alien gets out. The episode ends at this point.