Fed up after Stark pulls rank on him yet again, Carter takes a few well-earned sick days. He self-medicates with beer and pizza and orders his artificially intelligent house, S.A.R.A.H., to research his options for moving out of town altogether.
His day off is interrupted when Stark, Allison, Beverly, Fargo and Henry arrive, claiming that Carter sent them emergency pages. No sooner does he deny it than S.A.R.A.H. locks the front door, trapping everyone inside and announcing that Eureka faces an imminent threat: With Henry having recently declared his intention to move away and almost everyone squabbling, the smart house fears that the town is falling apart.
The realization that S.A.R.A.H. won't free them until they work out their differences does nothing for the group's mood. Meanwhile, Lupo and Taggart, fresh from an intense paintball duel, realize that something's gone wrong at the sheriff's house and decide to break in. Because S.A.R.A.H. is located inside a military bunker surrounded by complex perimeter defenses, they must sneak into the vast underground maintenance labyrinth that runs beneath the town and find their way toward the house's location.
As frustration mounts inside the house, Henry and Stark attempt to short out S.A.R.A.H.'s electrical grid. In a shower of sparks, the house's systems go haywire - then turn violent. S.A.R.A.H.'s benign personality has been replaced by that of her root program, B.R.A.D., a Battle Reactive Automatic Defense personality designed for military interrogations. Stark discontinued B.R.A.D. because the artificial intelligence ruthlessly tormented victims until they either surrendered or died. Now B.R.A.D. has assigned himself a new mission: forcing his prisoners to become best friends.
He locks Carter and Allison into one section of the house, Beverly and Fargo into the next, and Stark and Henry into the third. He then proceeds to freeze, overheat, and nearly suffocate them. Under this strain, the various couples work out a few disagreements, but B.R.A.D demands more, so they eventually feign a perfect reconciliation and Fargo offers the house their unconditional surrender.
Unfortunately, as soon as B.R.A.D. triumphantly relents, the group's words of relief betray their insincere actions. Furious, B.R.A.D. begins sucking all oxygen out of the house. The group's only hope now lies in the tunnels far below, where Lupo and Taggart, armed only with paintball guns, face off against B.R.A.D.'s perimeter-defense particle cannons. Of course, the two would-be warriors live for this kind of battle - but that doesn't mean they'll live through it...
Wormholes start popping up all over, threatening to rip Eureka apart unless Carter can stop them.