Frank has brought his son to The Sea to watch sports and they bond as John looks on. Then he takes off to "work" on a thrilling game of chess and a night on his own. The next morning he's greeted by a woman looking for him, with a child in tow. She thinks she knows him even though he can't remember him, and she has a boy with him – Wesley Silver, his son.
The woman, Althea, has a DNA profile of the father and it matches John's. Althea clears things up, explaining Wesley was conceived from John's donated sperm. She tracked down a medical history to a company named Vitrochoice who she then bribed for the DNA profile. Wesley is clearly highly intelligent despite being only 10 years old. John is tentatively thrilled and takes them to The Sea where Digger thinks it's some kind of scam. John goes to Vitrochoice to get into their confidential files by pretending to be a donor. Once he's in, he gets the fingerprint from the nurse and uses it to get to the computers.
John returns to his apartment and confronts Althea with the information that she was fertilized with eight different donors as part of a "Group OTTO" and even the doctors couldn't have given an accurate prediction of who the father was. John goes to hunt down the donors on the list and tries to do it on his own leaving Wesley behind, but Karen persuades him to take the boy along. Their first stop is a biker garage where he meets Dante Langenhan, one of the donors. Dante tells him to get lost. The next donor is a brain surgeon who Dante has already notified – clearly there's something up among the OTTO members. The third donor, D. Walker, is a woman who also tells them to leave. At the fourth donor's house, they find the door open and a dead man inside lying among piles of folders.
Frank arrives and they determine the man has been dead 24 hours and his brain was expertly removed. Avery and Frank aren't thrilled about John bringing Wesley and he shows them the list. They conclude that the brain surgeon, Elvis Braithwaite, had the skill necessary to remove the brain, and they turn up the murder of the fifth man on the list from six weeks earlier. They interrogate Braithwaite who has a temper, but he has the perfect alibi – he was in surgery the entire day of the murder. They also talk to D. (Dionne) Walker, who donated her eggs to OTTO. She reveals OTTO was a eugenics program designed to create super babies.
Althea and Wesley come to the hospital and John confesses he's unsure about being a father to anyone given his amnesia. Braithwaite, Dionne, and Dante are all together and demand that John prove his credentials as a genius up against the three of them – he passes. They then undergo a paternity test to determine if they're Wesley's parents, while trying to track down the last three donors, who had sent their sperm in by mail. And one of them could have been John.
The sixth donor, Zeke Pepperfield, started the OTTO program and bought a diamond mine in Arkansas…and diamonds are used in cranial saws like the ones used in the murders. They get an address and go there to find him dead. A hooded man goes running out and John pursues. The fleeing man is hit by a car but keeps going, rounds a corner…and disappears.
Wesley tracks John to the murder site and reveals he's color blind and John wants to get them tested. Wesley would rather have John show up as his parent at school to impress a kid, Jamie, but John isn't thrilled. Later he plays pool with John and they discuss the case and parenting situation. Digger wins the game and advises John to follow things up with Wesley. That night John takes Wesley to Jamie's house and makes it look like he's driving to impress the kid. He gets back and Karen tells him that one of the donor's house was broken into, so they all three moved into John's place.
After a less than restful night, the donor-geniuses recreate the chase and determine he ducked behind the billboard of an older building using loose bricks as a makeshift ladder. Inside the building they find the stored brains and bloody cranial saws. He also finds pictures of all the donors…and Wesley. At school, Wesley is watched by the man.
Back at the building, they get the news that Wesley has been kidnapped and find a journal of the murderer saying he will kill the project at its source, as it was an abomination. Once he couldn't get to the remaining donors, he went for Wesley and he's heading to Vitrochoice. John and the police go there where the killer is destroying the place and has Wesley strapped down to a table. The killer puts a saw to Wesley
but John cuts a power line and distracts the man long enough for Frank to shoot him.
They figure the killer is donor #7, Chris Sherman, leaving #8 as the last unaccounted-for donor. The donors are playing poker at The Sea and bonding when Karen shows up with the paternity tests. It turns out that Dante is Wesley's father and Wesley was lying about being color blind to convince John he was the father. Wesley is okay with Dante as a father and they head out, leaving John to consider his lost chance at fatherhood. Later a long-haired trench coated man meets with a bald man who gives him an envelope. The trench coated man then walks to an expensive car and gives the envelope to…Yellow Teeth. The envelope has surveillance photos of John and Wesley. She ponders the photos for a moment and then says, "It's time."