The events leading up to Matt's injury in the bomb blast begin shortly after the Christmas holidays. A syndicated columnist appears at General Hospital and requests an interview with Dr. Matthew Harmon concerning his life, his training, and his subsequent success as a surgeon who uses a wheelchair. The hospital board encourages the interview, saying it would be good public relations for the hospital and that Matt's victory would encourage other doctors who were facing the same problems. Reluctantly, Matt agrees to the interview, but insists that no personal questions be asked. This piques the curiosity of Dr. Chris Ramsey, Matt's colleague, who is trying to uncover secrets about Matt that could affect his chances to win the Quartermaine Residency Fellowship.

For several weeks Chris pretends to befriend Matt, all the while digging for personal information. Matt is very closed mouth with Chris about his past, but inadvertently, some facts leak out - Matt was from Detroit, he was injured in his sophmore year in high school, he transferred for his junior year to a school in Boise, Idaho, and contrary to what Matt has said about his past, he had no history in athletics. Chris also finds out that Matt was not injured in a skiing accident in Telluride, Colorado, as he claims. Due to financial problems and his need to win the fellowship and it's accompanying grant of $50,000, Chris becomes desperate to find more, and continues digging into Matt's past.

Matt's supervisor, Dr. Ellen Burgess, asks Matt to become involved in the treatment of a spinal cord injured young man, Keith Simmons, age 16. Matt sees himself in Keith, and he soon assumes a counseling role with the young man. Keith is very angry over his accident, and in trying to keep him from moving after surgery, Matt pulls some muscles in his back. Dr. Burgess insists that Matt have an x-ray to determine that the injury is not more serious. The x-rays reveal that Matt has bullet fragments imbedded near his spine, which would prove that Matt was not injured in a skiing accident, but was paralyzed by a gunshot. Chris asks Matt about the x-rays, and Matt states that he accidently spilled coffee on the x-rays and ruined them. All the while, the mystery surrounding Matt's past continues to grow.

Events come to a head in February, when Matt receives a phone call at work, advising him that "it's going down" and he has to leave immediately. He tells Dr. Burgess that he needs a week off for a "family emergency" and he leaves immediately, before getting her permission. Ellen later learns that he left town with two unidentified men.

We next see Matt entering a hotel room in Philadelphia with two men. They are Federal marshals. Matt protests that he will stay no longer than necessary. The marshals tell him to do his job and then he can go back to being "the good doctor." They order food from room service. When it arrives, Matt goes to the bathroom to wash up, and while he is there, a bomb planted in the food cart explodes, killing the two marshals. Matt is seriously injured. He awakens in a hospital in Philadelphia and learns about the deaths of the two Federal marshals. Against the advice of another Federal agent and the doctor, Matt leaves the hospital and goes back home to Port Charles.

By the time Matt returns to Port Charles, he is seriously ill with blood poisoning from his infected wounds. He calls the hospital and speaks with Grace. He tells her that he will not be back at work for a few days because he has the flu. Grace, thinking to do something nice for Matt, later brings him some soup. She knocks at the door to his apartment, but he refuses to let her in. She leaves the soup at the door. Suspicious, she returns later and insists that Matt let her in. He does so and Grace is shocked by his appearance. She reaches out to comfort him and he recoils in pain when she touches the place on his chest where he was injured in the bomb explosion. She tries to convince him to go to the hospital, but he refuses. Returning to the hospital, Grace informs Ellen of Matt's injuries and his illness.

Grace and Ellen go to Matt's apartment. He tells them that he was injured helping his cousin clean out a garage when a can of turpentine exploded. He convinces Ellen not to send him to the hospital, saying that he does not want to appear vulnerable and helpless to the other doctors. Ellen doesn't believe Matt, but she respects his wishes that he be treated, if possible, at home. Ellen and Grace run some tests and discover that he has blood poisoning that is raging throughout his system, and that his illness could be life threatening. Grace tries to convince Ellen to call EMS and get Matt to the hospital, but Ellen continues to honor Matt's wishes. She arranges to treat Matt with intravenus antibiotics at home. Matt becomes delerious. At one point, when Grace knocks to gain entrance to his apartment, he pulls a gun. Ellen is shocked and very concerned. In his delerium, Matt begs "them" not to send him ... somewhere. Ellen cannot understand, but in a sudden tender moment, she promises Matt that no one will make him do anything he doesn't want to do, because she won't let them.

In the meantime, Chris Ramsey suspects that something is very wrong. He insists that Grace is trying to hide something about Matt, and he appears at the door of Matt's apartment demanding entrance. Reluctantly Ellen lets him in. Chris takes one look at Matt and realizes that Matt is dying. He demands that they take Matt to the hospital where there are more life-saving resouces. Ellen agrees, Matt is taken to the hospital, where his wounds are treated, and this action saves his life.

While in the hospital, Matt, because he trusts Ellen, confides to her that he is not really Matthew Harmon. He tells her that he ran with an underworld mob when he was a teenager, and that he had witnessed a murder by the mob. In retaliation, the mob arranged to send him on a job that was botched, and he was shot in the back, and became paraplegic. He sought protection under the Federal Witness Protection Program, and began a new life. He told Ellen that he was called to Philadelphia to testify against the one remaining murderer who was being brought to trial. The mob found out that he was in Philadelphia and planted the bomb, which was meant for him. He told Ellen that they were looking for him, since they knew that he had escaped the bomb blast with injuries, and that when they found him, he would be a dead man. Ellen reminded a very anxious Matt that his identity of Matt Harmon was still obviously a secret to the mob, as he had been known by no other name since he came to Port Charles. The only thing that the mob knows about Matt at this point is that he uses a wheelchair. They do not know his new identity. Matt reasoned that she was right and he began to relax.

Chris Ramsey was determined to continue his dogged pursuit of Matt's past however, in an effort to uncover dirt on Matt that would keep him from winning the Quartermaine Residency. While Matt was hospitalized, Chris stole his apartment keys and went to Matt's apartment. There, he found a sales slip from a book store in Philadelphia that was dated during the time that Matt was absent from the hospital. He entered Matt's computer, and, through the Internet, learned from the Philadelphia newspapers that there had been a bomb blast in Philadelphia that involved members of the Mancusi family, Federal marshals, and an unidentified witness who had escaped the blast. Chris put all the clues together and reasons that Matt is part of the Federal Witness Program and is hiding his true identity. This information is enough to arm Chris with what he needs to intimidate Matt into leaving Port Charles and leaving the field free for Chris to get the Q Residency.

Matt receives a visit while in the hospital from Mike Corbin, owner of the The Recovery Room, and Matt's landlord. Mike, who has underworld connections of his own, and through his son, Sonny Corinthos, suspects that Matt might be in grave trouble. He tells Matt that if he needs help, then he (Mike) can help him - no questions asked. Matt denies that anything's wrong.

Matt recuperates sufficiently from the bomb blast injuries to return to work. Everyone, including Chris, is glad to see him. He renews contact with Keith Simmons, the young paraplegic patient, and promises Keith that he will not leave again. On his first day back at work, Matt opens his locker and finds an anomymous message that says "Hey, Matt, we found you." The message was planted by a gloating Chris, but Matt thinks that it's from the Mancusi mob, and that his life is in extreme danger. He immediately leaves the hospital and later shows up at Ellen's apartment.

Matt tells Ellen that he has come to say goodbye and that he has decided to go with the Federal agents who will give him another new identity. In a very sad and moving episode, Matt and Ellen reveal to one another their true feelings, and Ellen gives Matt a tearful goodbye kiss and embrace. Matt, himself moved to tears, leaves with the agents. He is doing what he has done once before - leaving everything behind that made his life worthwhile. It is an emotional moment.