The agency now works for the Beaurea of Indian Affairs. Their new sponsor has them investigate some strange activities on a reservation. They soon encounter an invisible creature. Secrets of the gland are revealed.
Someone is attempting to hack into the "Agency's" computer system to steal classified data. Eberts is sent into the field to assist computer ignorant Hobbes and Fawkes. Then things get worse when Eberts is suspected of being the hacker.
Hobbes, while undercover with Fawkes and Monroe inside the Post Office dead letter division, goes "postal" and starts shooting up the place. Hobbes ends up in the "psycho-ward" while Fawkes tries to figure out what caused it all.
Recalling how the previous invisible man's DNA was able to take over Darien when he was asleep. Darien asks Claire to find some samples of his brother Kevin, so he can remove the gland from Darien's head. Arnaud, permanently invisible, captures Darien/Kevin to have him fix his gland.
The Invisible Man goes undercover to infiltrate a gang of thieves who supply bomb parts to a dangerous terrorist. Darien is arrested and sent to prison with one of criminals in order to discover the terrorist's next move. Meanwhile, Hobbes and Monroe try to discover the location of a possible EMP device that could cripple modern civilization. The timer is ticking...
After wrenching his back, Darien visits an acupuncturist, in spite of The Official. Dr. Jay, however, accidentally triggers the Quicksilver gland and forces Darien to help her steal a Chinese artifact to save her dying mentor.
Darien cuts himself, and develops an infection. The bacteria from the infection are rendered invisible, believing they can mass produce the bacteria, they withhold treating Darien, but soon many people in the agency are affected. Worse since they withheld treatment for so long, the bacteria are now resistant to conventional treatment, so the infected people will go into Quicksilver madness /death. They race to find the cure.
After the Agency recovers a multitude of babies from a Chrysalis facility, Alex finds out some disturbing news about her son, who was among those recovered. This leads to her having to make some very difficult and painful decisions.
On an investigation, Dept. Of Weights And Measures' Special Agent Fawkes starts seeing a kind of apparition. Naturally everyone thinks he's going nuts. So he sets out to find just what the "apparition" actually is.
Hobbes and Fawkes must stop a very well trained government assassin who's "gone bad." But no one knows what he looks like. And when Fawkes eventually runs into the assassin, face to face, he finds something he never would have expected.
Eberts search to find funding for their Agency leads him to an agency that has many dead people on payroll. Hobbes and Fawkes look up an actual "live" agency employee, and end up trapped in a "community" from which there is no escape.
A person with a knack for selling secrets captures Claire, and injects her with a truth serum. It makes it impossible for her to keep quiet, or lie. She reveals several secrets, including the I-Man project. The truth serum will eventually kill Claire, Darrien and Hobbes race to find her.
By secretly accessing the SWRB's computers using Gaither's old password (that only he would know), Tommy Walker (AKA: Augustin Gaither), alerts the SWRB that Gaither is still alive. So the SWRB comes after Gaither in full force, while the "Official's" Agency has to try to protect and hide him and themselves.
Fawkes gets an injection that shuts off the quicksilver gland. But then the Agency has to find stolen "space-grown" crystals being used to make illegal drugs. So Claire and Fawkes struggle to restore invisibility to save a captured Hobbes.
Developing immunity to the anti-madness serum, Fawkes is given an untested new type before immunity becomes complete. But now it triggers stage 5 madness in less than a day, and shed quicksilver chips do the same to whoever touches them.
Claire disobeys the Official and gives Darien one last injection that fixes the gland, no more quicksilver madness. Darien goes to work for the FBI, and finds out about a plot by Crysallis. The FBI doesn't take him seriously, he needs Claire, and the Agency to stop Cryallis. The end of the series.