Empathizing with the plight of the wife and daughter of Jon Florence, a researcher at the Regional Infectious Disease Authority in Skokie, Illinois, who disappeared mysteriously, Jarod "Reilly" initiates a pretend as a virologist at the RIDA to find out what happened to him.
Jarod discovers that Jon Florence was going to expose Dr. Walter Garber's dangerous and unsanctioned experiments with level five viruses. To silence Florence and protect his research, Dr. Walter Garber sabotaged the decontamination shower and then exposed Florence to one of his mutated and deadly research viruses. After Florence died, Garber hid his body in the lab morgue. Afterwards, Garber blackmailed Jeff Baytos into keeping quiet about what happened, by telling him that the failure of the decon shower was his fault and that he was the one responsible for Florence's death.
After finding the unaltered security tape of the day in question, Jarod convinces Baytos that Dr. Garber deliberately murdered Jon Florence and enlists his aid in bringing the renegade researcher to justice.
We learn that the young Jarod and Sydney had a code word, "refuge," which Jarod could use to stop a simulation that was too frightening for him to continue. Now that Jarod is free, Sydney uses the word as a key in an e-mail to Jarod, to tell him that Sydney needs to meet with him.
After Sydney receives a box of newspaper clippings of catastrophic events and obituaries that can be attributed to the work he did while at The Centre, he visits a priest to seek absolution. Later, he also asks Jarod for his forgiveness. Jarod tells Sydney that he can't forgive him - he can't even forgive himself.
Because of Miss Parker's inability to catch Jarod, Mr. Raines reappears in her life. Raines tells her to bring Jarod back "where he belongs," or he will find someone who can.
Jarod gives Miss Parker a nasty case of the flu. He also discovers "roach motels" and creates a huge one in his room, that ends up trapping Miss Parker and her team by making their shoes stick firmly to the floor.