After some disputes with John Carmack about the design for Doom, he left to join Apogee/3d Realms. He was the game designer for Rise of the Triad, produced Terminal Velocity, and helped in varying degrees on Duke Nukem II and Duke Nukem 3D as well.
Next Tom co-founded Ion Storm with John Romero, and in July 2001 it was available on shelves. But the company was less than successful, and he and John founded Monkeystone Games, a company with far less grandiose plans. He designed, and Romero programmed, Hyperspace Delivery Boy, which was released in 2002. While Monkeystone still exists, he and Romero were hired by Midway Games.