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Time is running out for Darien in the onslaught of Quicksilver Madness, forcing the Keeper to give him a cure that frees him from the Agency.
Arnaud has a new scheme but when the team catches on, they have to negotiate with him to get a cure for Darien.
Not only is Darien gaining an immunity to the counteragent, but his Quicksilver Madness starts becoming contagious.
Fawkes gets a "cure," but is at a loss without his powers when a new case comes up that require his skills.
Darien is contacted by a Chinese "invisible women" who needs his help.
Tommy Walker begins to recover his memories, but another government agency wants him and will stop at nothing.
Claire is injected with a drug that forces her to babble wildly and lose her inhibitions, and will kill her if Fawkes doesn't find the cure.
Hobbes and Fawkes are imprisoned in "The Community" a hideaway for agents that can never go back into the outside world.
The NSA asks the Agency to bring in a rogue sniper, Forrester Purdue, and the Agency sends Darien and Bobby. Darien confronts the sniper, who can see him even though he's invisible. Fawkes recognizes the sniper as his father, who disappeared a long time ago. He goes to meet with his grandmother Madeline, and finds out apparently his father Mason did go to work for the government as an assassin. Investigating, the duo find out that Purdue's handler, Malachi Royce, was giving Purdue orders to kill folks for his personal reasons. When Darien's father refused, Royce had him declared rogue. Royce's men take Madeline hostage to lure out Mason/Purdue. After rescuing her, Fawkes confronts Royce and convinces him he'll take on his dad's assignment. Hobbes is Quicksilvered and invisible, and manages to get Royce on tape. After a brief father-and-son chat, Purdue disappears once again, leaving Darien hopeful they'll meet in the future.
While investigating out a water company as part of their new assignment as members of the Bureau of Weights and Measures, Darien spots the mysterious figure of a woman hovering over a computer...but only when he's invisible. He and Hobbes take the computer with them, and the ghost appears to Fawkes again, leading him back to the water company, and the ghost's daughter, Megan. Ordered not to investigate by the Official, Fawkes (naturally) investigates anyway, and discovers the mother was apparently killed in a particle accelerator "accident". The ghost, Lucille, has managed to hold herself together as a form of energy, but is only visible along the wavelengths that Darien can see when invisible. Darien discovers Lucille had discovered a means of creating cheap cold fusion, and her boss Dr. Henrick had her killed. Pretending to be the ghost, Fawkes tricks a confession out of the boss, but then gets knocked out by a lucky shot. Lucille traps her former employer in the particle accelerator and he dies the same way she did.
One of Chrysalis' "babycamps" is located, and Hobbes and Darien are sent in to get the kids out. Alex (still looking for her own son) gets word of the operation and goes in with them. They find Alex's child, only to discover she was an incubator: the child was actually the offspring of Chrysalis leader Stark and his wife. Darien follows Alex when she goes on maternity leave with her son, and thwarts a Chrysalis attempt to recover the baby. Then the child's biological mother Eleanor Stark shows up, and stops a plan to blow up Alex and child by a now nutso Stark. Eleanor helps out the Agency by getting info on Chrysalis (with a little invisible assistance from Darien). At the end, Alex gives up the child knowing it will be safe with Eleanor when she goes into the witness-protection program. Unfortunately, a few hours later they hear back that the agents guarding Eleanor and the baby are killed, and the mother and child have disappeared. Unknown to them, Eleanor never betrayed Chrysalis, but pretended so that she could get her and her husband's child back.
While getting his weekly Counteragent shot, Darien becomes infected with an experimental batch of Counteragent. The experimental stuff renders Darien randomly invisible...and it's contagious. First the Keeper becomes infected when she cuts herself while taking blood samples. She goes into Quicksilver madness, and attacks the Official. Both he and Hobbes becomes infected as well. Darien is also going into Quicksilver madness, since the arm with his tattoo is invisible. The Official locks down the facility under quarantine, but goes nuts as well, and escapes. Returning agent Alex Munro manages to capture him, and they discover that Hobbes is uninfected. The mayo on his sandwich was bad, and the bacteria counter-acted the experimental Counteragent. All they have to do to cure themselves is eat similar sandwiches with bad mayo...and get food poisoning for a couple of days.
During an attempt to stop Chrysalis from testing a stolen laser that generates lightning, Darien is shocked and gets amnesia. He turns himself in to the police but they try to arrest him based on his criminal record. Stark, Chrysalis' leader, takes Fawkes away and tries to convince him he works for the CIA. However, the amnesiac Darien is stolen away a third time by the invisible Arnaud DeFehrn, who convinces Darien that he is his similarly-invisible brother Kevin, and that they have to rescue their third brother, Johnny. Johnny turns out to be Huiclov, DeFehrn's brother, and the whole thing is a ploy to get Huiclov out of prison. Darien manages to regain his memory and capture Arnaud only to give into Quicksilver madness, and DeFehrn escapes. Stark figures out there is a second invisible man and contacts DeFehrn to make an alliance to restore Arnaud's visibility...and kill Darien.
During a mission Darien gets a back injury, and the Official refuses to pay for treatment. Seeking out an accupuncturist, Darien inadverently reveals he can become invisible. On his next visit, the accupuncturist, Charlene, inserts needles that allow her to use electricity to put Fawkes in agony if he doesn't obey her. She needs a rare set of mystical needles to cure her mentor, and Darien to steal them. He succeeds, but the needles have "bad chi" because the original owner, a millionnaire, stole them. The millionnaire has to be killed to eliminate the bad chi, but Charlie can't do it without gaining bad chi. So she forces Darien to try. Needing Counteragent, Fawkes manages to leave a clue so that the Agency can follow them, and prevent the murder.
Darien goes undercover as a thief to infiltrate the gang of the mysterious terrorist Javier and discover why they are stealing random parts. He and the leader of the gang, Dante, are captured and sent to prison, where Fawkes is left there to try and get the info from Dante. Pressured by two cronies from his previous stay, Darien promises to get them out by using his invisiblity to steal the warden's nameplate. Dante, impressed, also goes along with him. Darien breaks Dante out, while Alex and Hobbes manage to find the remaining members of the gang. It turns out the components can form an EMP bomb, but while the team manages to capture the gang, Javier escapes.
Darien is approached by Tommy Walker, a man whose senses (except touch) have been rendered inoperative. Using a special chest-mounted sensor device, Walker can get around, and can even spot Fawkes when he's invisible. He claims that he was another of Kevin Fawkes' experiments. Walker shows Darien some of the other experiments with sensory-deprivation performed by Kevin and his partner, Augustin Gaither. The other subjects went insane. However, a mysterious government organization, the Secret Weapons Research Branch, break in and claim everything is under their jurisdiction: even the Official is intimidated. They take Walker prisoner, but Darien believes Tommy can lead him to Gaither, who may know about Kevin's experiments and can find a way to remove the gland. Fawkes rescues Walker from the SWRB, only to discover that he is Augustin Gaither: he was driven insane by the same process when he used it on himself, and now believes he is "Tommy Walker". The SWRB blow up Hobbes' house where Walker is for safekeeping, but everyone manages to escape. It'll take years to restore Gaither to sanity, but when they do so it's possible he'll know the way to cure Darien.
After an operation goes bad and Fawkes goes into Quicksilver Madness, Darien realizes that there may be a way to find a cure. Despite the Official's orders not to, he has the Keeper inject him with some of his brother Kevin's memory RNA and channel his personality and memories as he did with Simon Cole (in "The Other Invisible Man"). The operation succeeds, but the RNA dates back to four months before Kevin was killed and Arnaud DeFehrn mutated the gland. Hobbes and "Kevin" track down Dr. Elizabeth Randell, who put the second gland in DeFehrn. DeFehrn beats them up and manages to escape, but "Kevin" is later kidnapped. "Kevin" fakes a fit of madness, knowing that the Counteragent will bring Darien back. Arnaud escapes again, but they get hold of a laptop computer with files on the gland. However, when they bring "Kevin" back for the last time to decipher the files, he refuses, believing Darien is a better person for it. Darien, needless to say, is less than thrilled.
Hobbes, Fawkes, and Alex go undercover since the Agency is now under the Post Office. They are sent to investigate thefts from the dead-letter office. When Hobbes opens an envelope with a card that plays "Jingle Bells", he goes berserk and shoots up the place. All of the team undergo psychiatric evaluation, but the only consistent factor in all their stories is the card. When Eberts opens it, he goes berserk as well. It turns out the card has a touch-transmitted chemical in it that, in conjunction with the song, turns the victim into a berserker. The card was sent to the post office by some 60's anti-establishment type and was leftover until someone found it. Fawkes manages to stop Eberts, and Hobbes is given a clean bill of health.
Fawkes, Hobbes, and Alex are sent to bring in a kid, Adam Reese, for testing. After thwarting a Chrysalis attack, Alex explains that Adam has an Ebola-like retrovirus as part of a government experiment that will become active when he hits puberty. Darien manages to convince Adam to come in for the tests anyway. Unfortunately, the government simply plans to incinerate Adam. Hobbes and Fawkes help Adam escape, and manage to steal a cyrogenic pod (last seen in Frozen in Time) from Chrysalis. Adam goes into suspended animation rather then unleash the virus.
Hobbes and Darien investigate a hacker trying to break into the Agency computer system. The hacker escapes, and Eberts manages to suggest being allowed to tag along with the team as a computer expert. He and Fawkes sneak into a internet cafe but are ambushed. Knocked out from behind, Eberts is taken back to the Agency and soon starts to act increasingly aggressive, going so far as to ignore the Official when inevitably told to "Shut up, Eberts!". Eventually Hobbes and Fawkes discover that Ebert has been replaced by their invisible nemesis Arnaud DeFehrn. DeFehrn gained cell samples of Eberts during his last physical, and used them to make up a lifelike skin mask. He needs Eberts' access to get into the Official's computer. After a bicycle & skateboard chase, DeFehrn manages to elude Darien, leaving the Agency to wonder when DeFehrn will show up again.
The Agency is now controlled by the Department of Human Services. 5-Star A-rated agent Alex Munro comes barging in, taking control of the place. She knows everything about everyone, but her own record is murky. Her first case is to have the Agency investigate the disappearance of babies from hospitals. Fertility clinics owned by the same corporation are the key factor. The team prevents an abduction and tracks the abductor to a summer camp where children are being raised from birth and brainwashed by the Chrysalis organization. A standoff between the Agency and the armed children ensue, but Darien breaks the stalemate by entering the compound and calling for Chrysalis leader Stark. Darien convinces Stark to release the children rather then have them get killed. The children turn themselves in, but Stark escapes as part of the deal. It turns out that Alex's baby was one of the abductees...and her child isn't among the residents of the camp.
Darien, Hobbes, and the Keeper are sent to investigate the brutal deaths of several Indians and suspect that Bigfoot might be involved.
