Before this, he was a lieutenant himself, serving as superior of, and best friend of, Harry Morgan. When Harry committed suicide, apparently having burned out from witnessing too many failures in the justice system, Matthews used his influence to bury any indication of suicide, and fulfilled a promise he made to Harry to look after Dexter and Debra; which is what he has done to this day.
Matthews is portrayed as having flaws: While having originally promoted LaGuerta, he frequently clashed with her, trying to keep her focused on hunting the Ice Truck Killer correctly. Later, however, he fails to take his own advice, as, when Neil Perry was mistakenly arrested, and Matthews received all the praise, he went so far as to try to bury any evidence to the contrary.
Seeing the investigation was being jeopardized, LaGuerta revealed that several mistakes during the Ice Truck Killer case had been made, landing Matthews in a world of trouble. Due to the fact he was friends with both the police commissioner and the review board, Matthews escaped punishment and, having been personally embarrassed and wanting vengeance, Matthews laid all the blame on LaGuerta, and so gained approval to install Esme Pascal as the new lieutenant; to supervise her.
This proved temporary, however, having later seen Esme break down and regained his confidence in LaGuerta's abilities, Matthews restored her to her previous position. Matthews' latest political effort, applying for the position of deputy chief, succeeded after Matthews used the fame of successfully ending the Bay Harbor Butcher case to propel himself to that position.
Matthews did not appear in Season 3, but re-appeared in Season 4, having succeeded in being promoted to deputy chief, personally invested in the investigation surrounding Frank Lundy's death, and Debra's shooting. After LaGuerta and Batista reveal their relationship, he initially wants to transfer Batista out of Homicide to avoid complications during a trial. Eventually, LaGuerta and Angel both agree to end their relationship to continue working in Homicide; and while accepting this, Matthews warns them that there will be serious consequences if their relationship continues.
After revealing a video of LaGuerta and Batista kissing, LaGuerta calls Tom out, asking if it was because of her gender or race that he seems to have a grudge against her.
Matthews simply replies he has a grudge against her because of her arrogance. In order to circumvent a reprimand from higher up, and also as a result of their deepening feelings for one another, LaGuerta and Batista secretly get married with Dexter as witness.
In the sixth-season premiere, Matthews oddly has promoted LaGuerta to captain, which many characters note as unusual. After the ceremony, however, it is shown that LaGuerta had found a "little black book" of a brothel with Matthews' name in it, trading the evidence for her promotion. Accordingly, her promotion left the lieutenant position open, which LaGuerta attempted to secure for Batista. However, Matthews declares Debra a more suitable candidate, being young and famous after a shootout at a restaurant in which Debra and Quinn were involved was recorded and posted online.
LaGuerta and Batista both believe that he did this in vengeance, though little was proven. His prostitute-hiring tendencies leads to a call girl dead from a heroin overdose, which while not his fault, led to LaGuerta attempting to cover up the no-fault crime scene claiming the low clearance rate as unacceptable. However, Debra continues to search after a visit from the call girl's parents, leading to her discovery of Matthews' involvement. LaGuerta used the information on Tom and betrayed him and had him forcibly retired by the board when she told them.
Tom however, believed it to be Debra who sold him out but she stated she never would do that and Debra would confront LaGuerta for doing such a low tactic, knowing full well she did it for her own personal gain. He is seen on his boat drinking scotch greeting LaGuerta as she confides her suspicion that the BHB is alive and well.
Tom doesn't believe her, stating the evidence was all against Doakes, but seems to show surprise after hearing a blood slide was found at Travis Marshall's church site. Though reluctant at first, Tom decides to help after discovering LaGuerta was the one who sold him out to the board and shows his anger despite LaGuerta stating he started it.
He intends to help for his own reason for his year pension despite LaGuerta's displeasure at the prospect. As they dig into the case, they revisit the cabin Doakes died in and discover that Santos Jimenez had rented the cabin, prompting Tom to realize who he is and reveal to LaGuerta that Jimenez is responsible for Dexter's mother's death and changing Brian, Dexter's brother, into becoming the ITK. Tom however, refuses to believe her and prevents LaGuerta from questioning him, stating he'll do it having known Dexter since he was a boy.
As Tom talks personally to Dexter, he confides how LaGuerta believes he is the butcher though Dexter is able to see that Tom also believes it in some way. Dexter then tells him about a boat Doakes once had to lead him off the case which has Tom believe him. He tells LaGuerta about this and she doesn't believe him stating she would have known if Doakes had a boat.
They find a tackle box from the old cabin and find a key to a marina and, believing it to be Doakes's old boat spot, search the area and find several sheets of plastic, knives and one with degraded blood on it with Doakes's fingerprints on it. This causes Tom to immediately believe Dexter, but LaGuerta still believes otherwise stating Dexter could have planted which is actually true it despite Tom's refusal and that Maria should move on.
She says she'll keep her word and give Tom his pension and later is visited by Dexter where the two make amends for each other's suspicions.