After the events of "Forever Red", Tommy becomes a science teacher at a school in the (fictional) city of Reefside, California at the onset of Power Rangers Dino Thunder. A trio of students in detention — Conner McKnight, Ethan James, and Kira Ford — unravel Tommy's past as a Power Ranger after uncovering three artifacts from his lab that turn them into the Dino Thunder Power Rangers. Tommy recruits these students to become the Dino Rangers, doing so while seeming mysterious and somewhat obnoxious, as noted by Conner. When he discovers that Mesogog is still active, he joins the other Dino Rangers and becomes the Black Dino Ranger, aided by the power of invisibility from the Black Dino Gem. His Dinozord is the Brachiozord carrier, he wields the Brachio Staff, and he drives the Black Thunder ATV (originally devised as a trap by the then-evil Trent Mercer, but it was soon reprogrammed).
When the White Dino Ranger appears, Tommy's dedication to saving the lives of innocents seems to give Tommy cause to show no mercy to him, even after he discovers that the White Dino Ranger is Trent Mercer. For a while, he is encased in amber by the White Dino Ranger, and once freed, finds himself unable to de-morph, due to his Dino Gem and his morpher re-molecularizing. He remains in his morphed form for a while. Despite this resolve, he could not help but feel sympathy for Trent when his students did not, reminding the others of his tenure as the evil Green Power Ranger.
After seeing the power of the White Ranger Clone and the Terrorsaurus, Tommy decides that the Rangers need an upgrade. He takes Trent to the location of the Shield of Triumph, as the shield can only be freed from its resting place by the power of Trent's Dino Gem. He also has a hunch that Conner is the one destined to control the shield. His assumptions are proven right, as Conner shows up just in time to save the shield from being lost forever. Tommy informs the other Rangers they have to contribute their energies to the shield, and Conner becomes the Triassic Ranger.
He is later de-morphed by a special substance, but is rendered invisible as a result. An experiment sees the return of Tommy to his natural state, but the process shatters his Dino Gem and leaves Tommy in a coma. During this time, Tommy endures several internal battles, facing off against several of his past Ranger alter-egos: Zeo Ranger V, the White Power Ranger, and then the Green Power Ranger. After proving that he would not give up the fight for his life, his opponents each offer him a shattered piece of his Dino Gem. Tommy regains consciousness holding the newly repaired Gem in his hand. As a result, he also gains access to his Super Dino Mode.
While he mentors the four Dino Thunder Rangers, he shows a particular interest in the current Red Ranger and leader Conner McKnight. Tommy often brings up the striking similarities between Conner and himself when he was a Ranger. Because of this, he puts a lot of faith and trust in Conner and is more than willing to offer him advice. He especially brings this up when Conner is doubting himself and talking to him about passion and the endless limitations of that passion. With that help, Conner is able to unleash his Battlizer mode through his own willpower.
When he learns that Trent has been hiding his father's secret identity, Tommy considers asking Trent to surrender his Morpher. Though Tommy comes to understand Trent's loyalty, he leaves the decision of letting Trent stay with the team to the other Rangers. They decide to let Trent stay after he saves Conner's life. In a final battle against Zeltrax, Tommy advises the Rangers that the only means to succeed is to sacrifice their Zords. At the end of the series, Tommy, alongside Kira, destroys Zeltrax. The Dino Rangers sacrifice their Dino Gems in order to destroy Mesogog's ultimate form(s). By that point, Mesogog has already managed to separate himself from Dr. Anton Mercer. In the end, Tommy answers Anton's question of what he would do now by insisting he would pursue the simple life of a high school science teacher, finally retiring his life as a Power Ranger for good.