In the 2003 cartoon, T.C.R.I.'s original branch was in Japan, but Yukio Mashimi, one of the Guardians, betrayed the Utroms to the Utrom Shredder, so they withdrew to New York in North America. They continued work on their transmat during this time, which resulted in the production of a mutagenic waste product. On a fateful day, a company truck lost a container of mutagen in the sewers, even as four baby Turtles also went down.
Some fifteen years later, the T.C.R.I. building came under the scrutiny of those same mutated Turtles, and they managed to infiltrate it. During a conflict with the Utroms, they accidentally activated the transmat, causing a massive energy burst to emanate from the building. This brought T.C.R.I. to the attention of the National Guard and the Utrom Shredder.
T.C.R.I.'s facility was then surrounded by the Guard, which prompted the Utroms to begin evacuation back to their home world. The building—and presumably the corporation—were destroyed shortly afterwards.