A former Centre operative has been killing innocent people, using simulations that Jarod performed while still a captive at The Centre. Jarod and Broots work together to stop the rogue before he uses the deadliest of all the simulations and releases a strain of the Ebola virus that Jarod created.
Broots' new computer security system indicates that a mole at The Centre has been downloading information, using the relatively low security Centre Data Annex to pass it on to his partner on the outside. Miss Parker sends Broots to the Annex find out the identity of the mole and to determine what kind of information has been leaked.
When the person behind the espionage realizes that his activities can be traced, he kills everyone at the Annex in order to cover his tracks. Broots is at the Annex when the assassin arrives, but survives the melee because he was in the bathroom. As Broots runs for his life, Lyle declares him a "Schedule 7" - which means that no one from the Centre will bring him in. Broots is on his own as the thief attempts to tie up the last loose end at the Annex by tracking him down and killing him.
Jarod knows who is behind the theft of his simulations - it's Damon, a one-time Centre employee. To get the Pretender to finish a simulation, he had once threatened harm to a janitor Jarod had befriended. When Jarod capitulated and gave Damon the simulation The Centre wanted, Damon murdered the janitor anyway, telling Jarod not to make things so difficult next time.
Since The Centre has declared Broots persona non grata, Jarod finds the terrified tech and takes him back to his lair. Together, they use the information that Broots' security system obtained, along with a delivery code discovered at The Centre (passed along by Sydney), and determine where and when Damon plans to use the final simulation.
During the ensuing confrontation between Jarod and Damon, Jarod finds himself reliving the situation that occurred at The Centre years before and has to kill Damon to stop him from murdering Broots.
Unable to override Lyle's "Schedule 7" on Broots, Miss Parker does the next best thing - she retrieves Debbie from school and has Sam keep her safe at her home. When Broots is exonerated, he gives Debbie her birthday present, the trip to Paris for which she has longed.
Broots discovers that Jarod eats the same thing for breakfast that he does, Pop Tarts.