In the 2003 television series, the Federation is a civilization in a far-off galaxy, dominated by human-like aliens.
The Federation is one of the two dominant civilizations in the galaxy, with the other being their enemies in the Triceraton Republic. Many planets are under their rule, and its military head General Blanque shows a keen interest in conquering even more.
One scientist working for the Federation military was Professor Honeycutt, who developed plans for the teleportal, a teleportation device similar to the Utrom transmat. However, he was unwilling to actually build the device, as General Blanque intended to use it as a tool for military conquest and warfare. Unfortunately, he was accidentally transferred into the body of a robotic assistant, leaving him with no rights under Federation rule. Blanque immediately mobilized Federation troops to capture the "Fugitoid."
The Turtles came into contact with the Federation when they were accidentally sent to D'Hoonnib by a transmat. They arrived just as Professor Honeycutt was about to be apprehended by a squad of Federation soldiers, whom the Turtles easily defeated. They became fugitives alongside Honeycutt, and were pursued by Federation forces.
However, Honeycutt was instead captured by the Triceratons, who had been informed of his existence and his teleportal plans by Blanque's aide Lonae. Blanque led a fleet to retrieve the Fugitoid from Triceraton territory, arriving just as he and the Turtles escaped the Triceraton gladiatorial arena. A battle broke out between the two sides, during which Honeycutt and the Turtles managed to escape the area. As they closed in on the escapees, their quarry were transported to Earth through a transmat.
However, the Federation were able to track the transmission back to Earth. They secretly met with the Earth Protection Force, offering alien technologies and the Turtles in exchange for the Fugitoid, Upon capturing Honeycutt, they attempted to extract the teleportal information from him directly, only to discover that he had already deleted the plans. Furthermore, the Federation's base was then taken over by the Fugitoid, who infected the Federation computers with a virus that debilitated their fleet before also infecting the Triceraton ships.
The Turtles successfully captured General Blanque, removing him from power. He was subsequently imprisoned along with Zanramon, and the Federation soldiers were treated as honored guests as the first gesture towards peace.