The Transmat is an Utrom invention similar to Professor Honeycutt's Teleportal in the 2003 TV series, and the games Teenage Mutant Ninja Turtles 2: Battle Nexus and Teenage Mutant Ninja Turtles Smash-Up. It teleported the turtles to another world, and eventually was used some weeks later to pull them back to Earth along with the Fugitoid. As the National Guard investigated the TCRI building, the Utroms were forced to begin evacuating the premises through the Transmat. The aliens successfully returned to their homeworld, and the Turtles were able to use the device to escape the Shredder, teleporting themselves a safe distance. The Transmat was then destroyed in a massive implosion.
In the episode Same As It Never Was, the alternate future Ch'rell forces the Utroms to build one for him. With it, he planned to send forth his armies and enslave the stars, one world after another. But he was killed by Donatello before he got a chance to put his plain into action. It's revealed in the episode Secret Origins that the waste products from the Transmat are the Ooze that caused the Turtles' mutation.
In the game Teenage Mutant Ninja Turtles Smash-Up, The Shredder captured Fugitoid in order to force him to make a Transmat to teleport his armies all around the world. At the end of the game Honeycutt flips the switch on the Transmat, which Shredder and Karai have landed on, and teleports them to parts unknown.