While in the midst of a pretend as an orthodontist, Jarod sees a news report on TV about an escaped convict who turns out to be his childhood friend from The Centre, Kyle.

At The Centre, Miss Parker, Sydney and Broots are giving Angelo all of Jarod’s red notebooks in the hope that once he “absorbs” Jarod’s complete personality from them, he’ll be able to tell them where to find Jarod. When Angelo “absorbs” a blue notebook that was among the red ones, he unexpectedly bursts through a plate glass door and attacks Miss Parker.

Sydney explains to Miss Parker that the blue notebook belonged to another pretender - Kyle. Although Kyle had been "officially" released from the pretender program, he had then fallen into Raines' hands and been kept on SL-27 long enough to have been turned into a sociopath who Raines successfully stripped of all morality and conscience. Eventually, this led to Kyle committing a string of violent felonies that culminated with the kidnaping of a nun (Harriet Tashman), followed by his capture and imprisonment.

Jarod quickly infiltrates the prison from which Kyle escaped, posing as a criminal psychologist, in order to be able to examine Kyle’s cell. Shortly afterwards, Special Agent Jarod Ness joins the FBI detail searching Harriet Tashman’s home for clues to determine whether Kyle kidnapped her or she fled on her own. Later, while watching a 10 year old tape of the news report of Kyle’s original abduction of Ms. Tashman, Jarod sees his mother hurrying up to comfort her and is astounded to realize that Harriet Tashman knew his mother.

Using a picture he found among Kyle’s prison cell correspondence, Jarod locates Harriet Tashman’s second residence, a farm in upstate New York. He learns from the caretaker there that his mother and father lived in a room over the barn - hiding. Jarod examines the room, and finds a bookmark in a Bible that matches one that he saw in a book at Harriet Tashman’s house. The bookmarks lead Jarod to Saint Catherine of the Hills Convent, where he arrives just in time to see Kyle repeat history by abducting Harriet Tashman.

When the FBI agent in charge (Agent Korkos) issues a “shoot to kill” order on Kyle, Jarod leads Korkos team on a wild goose chase by making them think that Kyle is in Boston.

Broots is able to reconstruct the DSA’s of two of the sims that Raines had Kyle conduct while on SL-27. The second one, recorded in 1970, shows Mr. Raines teaching Kyle to hate, while the young boy is using a life sized cardboard cut out of Catherine Parker for target practice. Miss Parker begs her father to allow her to bring him “living” proof of Mr. Raines wrong-doing, in the form of Kyle.

After finding a picture of a dragon in a blue notebook left by Kyle at the convent when he abducted Harriet, Jarod calls Sydney and tells him that he needs answers about what it means, now. After he has Broots hack into Mr. Raines computer, Sydney gives Jarod the news that the Dragon House is a Centre safe-house, located in Delphi Shores, New Jersey. He also warns Jarod that Mr. Raines and Miss Parker won’t be far behind him in getting there.

Jarod finds Harriet Tashman at the Dragon House, where Kyle is threatening her with battery cables in order to make her reveal the information that he wants from her. Jarod attempts to free Harriet, but Kyle stops him. Their standoff is interrupted by the arrival of Mr. Raines and his team of sweepers. Kyle creates a diversion by shooting the battery. Both he and Jarod flee in separate directions, only to end up facing each other again - this time outside, on the balcony. Once again, the standoff is interrupted - first by Harriet Tashman, who makes Jarod lower his gun, then immediately afterwards by the arrival of Miss Parker and her team. Miss Parker directs her team to go after Kyle, and Jarod and Harriet Tashman get away.

As the sweepers take Kyle down, and then into custody, Miss Parker sees Mr. Raines standing up on the balcony. Meanwhile, in their car, speeding away from the Dragon House, Jarod asks Harriet Tashman why she risked their lives by making him lower his gun. Harriet tells Jarod that she couldn’t let him shoot Kyle, because Kyle is his brother.

Jarod discovers Highlights, a children's magazine, and two cartoon characters featured in it, who are named Goofus and Gallant.

At Harriet Tashman’s farm, she explains to Jarod how she came to be associated with his parents, Margaret and Charles - and his sister, Emily, who was born a month after his parents arrived at the farm. She also tells Jarod that, somehow, Kyle found that Harriet had ties to his parents, and began threatening her - but since she never knew who Kyle was, even when he abducted her, she didn’t tell him that Charles and Margaret were on her farm. They moved away a month after her abduction.

Thinking about their time at The Centre together, Jarod remembers the night Raines took Kyle away. Someone pushed the flying cross medal that Kyle always wore on a chain around his neck through the ventilation grate into Jarod’s room. Jarod hid it behind his sink.

Miss Parker, meets Sydney and Broots at The Centre’s Hybrid Biotract 42 where she enlists their help in getting to Kyle. Kyle tells her that he was not the one who killed her mother, but doesn’t deny it when she asks him if Raines was the one who did.

Harriet Tashman tells Jarod that she might know someone who can help him find his parents, but she won’t say who it is and will only contact them herself. Jarod tells her that he is going back to The Centre to get Kyle.

Jarod breaks into the Centre and leaves the word "REFUGE" spelled out in PEZ on Sydney's desk. Before going to find Kyle, Jarod goes back to his old room and checks to see if Kyle’s medal is where he hid it - behind the sink - but it isn’t there. A moment later, it is dangling from the ventilation grate again - but this time, Angelo reveals himself to Jarod. Angelo drops a box of his Cracker Jacks on the ground and Jarod realizes that Angelo is “C.J.”, the person who stayed in contact with Kyle while he was in prison.

Angelo leads Jarod through the ventilation ducts and he arrives in Kyle’s room, explains that they are brothers, and frees Kyle before the surgeon that Raines intimidated into performing a frontal lobe separation on him can do his job. Angelo sacrifices his chance for freedom, in order to make sure that Jarod and Kyle escape by causing Centre security to chase after him instead.

Miss Parker is desperate to get both Kyle and Jarod back. She gives Angelo the notebooks and files of both men, so that he can become both of them at one time and tell her where to find them. From the Harriet Tashman abduction file, Angelo gives Miss Parker a picture of Harriet’s farm and indicates that she will find Jarod there. Unknown to Miss Parker, Sydney and Broots, Mr. Raines is watching from above.

Jarod takes Kyle to Harriet Tashman's farm. In their parents’ room above the barn, they discover a mobile of origami swans in Emily’s cradle. Soon afterwards, Harriet Tashman returns from her trip with good news, but Raines has already phoned the FBI and told them where they can find “John Doe.” Before Harriet can tell Jarod and Kyle anything, they all forced to flee in a van, with Agent Korkos firing at them from behind. One of his bullets finds a tire and the van flips over. Again, Jarod and Miss Tashman escape, but Kyle is trapped, unable to run because of a broken leg. He gives Jarod back their fathers flying cross medal, and asks him to not let their parents know what he became. There is an exchange of gunfire and the van explodes after the gas tank is ruptured by the bullet. Jarod believes Kyle to be dead.

Harriet tells Jarod that his parents are in Boston and gives him a paper that has the address and time of a meeting that she has set up to reunite them. The next day, at The Centre, Miss Parker sees her father giving Mr. Raines a piece of paper that has a possible location for Jarod on it. He tells Raines to take a sweeper team and bring Jarod back.

In Boston, Jarod is heading toward the meeting place on foot, unaware that he’s being closely followed by Willie and Mr. Raines’ other sweepers. Miss Parker arrives with Sydney and Broots. She makes sure that they are both armed and they split up, trying to find Jarod.

At the assigned meeting place, a taxi pulls up and Jarod’s mother gets out. His sister pokes her head out of the back seat - looking for Jarod. Jarod sees his mother and his sister - and they see him, but before they can meet, Raines’ sweepers interfere. Margaret and Emily escape in the taxi in which they came. Jarod disarms one of the sweepers and runs down an alley, only to find Mr. Raines blocking the other end. Jarod screams at Raines, saying that he stole him from his parents, had the FBI kill his brother and now he’s trying to kill his family. Jarod wants to know what he has ever done to Raines. Raines replies, “You exist.” Jarod’s hand is trembling with the desire to pull the trigger on the gun that is in it. But he does not. He won’t let Raines to do him, what he did to Kyle.

As Jarod turns and begins running away, Raines pulls out a gun of his own, intending to shoot Jarod in the back, but an unseen shooter fires at Raines' and hits his oxygen tank, causing an explosion that severely burns Raines.

At The Centre, Mr. Parker is summoned by telephone to report to Mr. Lyle on the recent events. Miss Parker watches as her father is escorted away by sweepers. Broots reports to Miss Parker and Sydney that an investigation into the shooting could not reveal which from gun the bullet that hit Mr. Raines’ oxygen tank was fired.

Jarod calls Sydney. Sydney tells Jarod that no remains of Kyle were found in the van and reminds Jarod that The Centre will be more determined than ever to find him and bring him back after all that has happened. Jarod replies to Sydney, "Catch me if you can." In Jarod’s sunglasses is the reflection of the space shuttle, climbing upward, as in the background, the sound of the rocket booster engines grows louder and louder.

Guest Stars: Linda Carlson (Harriet Tashman), David Doty (Appartment Manager), Bernard Hocke (Dad), Ryan James (Boy), Augie Kirkland (Grey Guard), Michael MacLeod (Peter), Kelli Maroney (Reporter), Cody McMains (Ike), Jason Ronard (Driver), Doug Spinuza (???), Thomas Tofel (Surgeon), James Tolkan (FBI Agent) and James Wellington (Blue Guard)