When Olivia discovers that she's run out of migraine medication, she goes to the local pharmacy to have her prescription refilled. As she goes back to her apartment, she spots Lincoln in a diner and goes inside to talk to him. He admits that he hasn't been able to sleep since he came to Boston and joined Fringe Division, and admits that he's had trouble coping with the knowledge that he's gained of Fringe activities. When Olivia says that it will become a part of him eventually, he asks if that's what happened to her.
Jack is walking home and calls his wife, Meg. He says that someone is following him and she calls the police. Jack loses the phone signal until he gets to his apartment, and Meg tells him that the police are on the way. As he opens the front door, an invisible man grabs him and shoves him inside. Two minutes later, two officers arrive to investigate and find Jack dead, his skin and hair bleached white. The invisible being tries to slip by them and one of the officers opens fire. He misses, and Meg arrives to realize that her husband is dead.
Peter is shopping with an escort, Agent Tim, and unhappy that he has someone tagging along. When Peter tries to help a young boy, Tim intervenes and admits that he's been told to prevent Peter's interaction with civilians.
Olivia, Lincoln, and Astrid are summoned to the apartment and Broyles briefs them on what happened. While Astrid examines Jack's body and confirms that the neck was broken, Olivia and Lincoln talk to the officers. The one who shot is reluctant to admit what happened until Lincoln assures him that they'll believe whatever he has to say. He reluctantly admits that he may have seen a ghost. While Lincoln checks the glass from the shattered front door, Olivia asks Astrid if what they see day in and day out bothers her. Astrid admits that she sees a shrink and asks who Olivia talks to, and Olivia admit that she doesn't talk to anyone and she's starting to realize that it's strange. Lincoln comes in and tells them that he's found a trace of blood on the glass, meaning the killer is human, not a ghost.
In a basement somewhere, the invisible man is immersing himself in chemicals. After a few minutes he turns visible, much to his relief. He puts on a suit and goes to a building. He gets in the elevator but discovers that he's starting to disappear again.
At the lab, Olivia checks the police files and finds three other murders of individuals suffering from albinism. Walter checks Jack's body and finds a residue of chromatophores, which are used by certain animals in nature to blend in with their surroundings. Astrid finally gets a match on the DNA of the blood sample and traces it to Parkview Hospital and Baby Boy Bryant, who was born in 1989 and only lived four days before dying of a genetic abnormality. However, Jaffe admits that as the baby was taken away, she thought she heard it crying. When she mentions the name of the private insurance company, Olivia recognizes it as Cyprox Inc., which also funded her mother's treatments when she was dying of cancer. As they leave, Olivia tells Lincoln that Cyprox was part of a company that became Massive Dynamic.
At Massive Dynamic, Olivia and Lincoln meet with Nina, who immediately confirms that the baby was the subject of genetic experiments because of his unique condition. They administered chromatophores into the baby's skin, hoping to make a human spy who could blend in perfectly with his surroundings. The treatment also saved Bryant's life. Nina then tells the agents that the baby, nicknamed "Eugene" for "Unique Gene," apparently died in a lab fire in 2001.
At the apartment where Eugene leaves, the woman from the elevator, Julie, goes to her apartment. She's unaware that the camouflaged Eugene has entered behind her. Julie relaxes for some music and calls to her cat, but gets no response. When she goes to the bedroom, she discovers that the bed is covered in leaves. Someone runs out the door and Julie hastily locks it.
Peter is working at home on schematics for the Machine when Lincoln arrives with more plans. Peter thanks him for treating him as a normal human and explains that he hopes to use the Machine to return to his own timeline. Lincoln is somewhat overwhelmed at the idea of alternate timelines and points out that Olivia isn't phased by any of it. He admits that Olivia is like no one he's ever met and Peter agrees. When Lincoln asks if he was involved with Olivia, Peter says that he was with the one in his timeline, and that the Olivia in this timeline isn't the one he knows.
Lincoln is called back to the lab where Walter is experimenting with an octopus. They realize that Eugene is killing to steal pigmentation to restore himself to "normal," and Walter returns that he will need a great deal of it... and produce many more victims.
Eugene attacks and kills a man in the parking garage of his apartment building.
At the lab, Walter informs the others that Eugene will kill himself if he manages to restore his pigmentation, and tells them that they can use ultraviolet light to spot Eugene. The agents are summoned to the parking garage and confirm that no one has gotten out past the doorman. A police dog picks up Eugene's scent at the door and they realize that he's in the building's upper levels. They bring in more dogs and evacuate the building, and then shut down the elevators. The agents split up to search the building and Olivia wanders into a construction zone. She falls into a shaft and just manages to catch the edge, and Eugene emerges from the shadows. He tells her that it's important to be seen, and then pulls her up. Eugene takes her gun and Olivia explains that he's dying. Eugene doesn't believe it and figures that she wants to take him back to the military for more experiments. Olivia says that Walter can cure him at the lab, but Eugene refuses to return to a lab, any lab.
Lincoln and the other agents arrive on the floor and Eugene runs into the shadows. They lose him and conduct a thorough search, but have no luck. As Broyles has his men let the residents back into the building, the dogs start barking. Olivia looks around, unaware that Eugene is visible again and has slipped out as one of the residents. Inside, the agents find the sub-basement and the room where Eugene lived and experimented with the pigmentation. Olivia finds a shelf filled with tokens that Eugene took from all of the residents and realizes that he wants to be seen, not cured.
Later, Eugene restores himself to visibility one last time and then goes to the elevator and gets in with Julie. She takes notice of him for the first time and hopes that he wasn't sick because it's such a beautiful day. Eugene agrees with her and watches her go, and then dies.
Olivia reports to Nina what happened and that they found Eugene's body. She worries that just like Eugene, she may not be normal and that her emotions may have been stunted by cortexiphan treatments. Nina assures her that she's normal despite the treatments, and that Olivia just has to find her way in the world. After a moment's consideration, Nina admits that her life before she adopted Olivia and Rachel was nothing but work, but now she can't imagine her life without them.
At Fringe Division, Peter stops by to see Lincoln and gives him a present in return for his treatment of him as normal. Lincoln stares at them, puzzled, and Peter says to trust him. As he leaves, Olivia stops by Lincoln's desk to get some paperwork. She suggests that she might stop by the diner if he can't sleep and is there that night, and Lincoln agrees. Once she leaves, Lincoln tries on Peter's present: a pair of more stylish glasses.
That night, Lincoln is at the diner. Olivia is preparing to go out to meet him when someone pumps knockout gas into her apartment. Once she collapses, two men come in, tamper with the security camera, and give her an injection so she won't remember the last two hours. They then leave... with Nina Sharp.