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In the Mirage comics he was a ruthless leader who led the war against the Federation of D'Hoonib. To that end, he sought a teleportal device created by Professor Honeycutt to use against them and captured him along with the Turtles who were with him at the time. The Turtles managed to free themselves from their captivity and take Zanramon hostage. Unfortunately, Zanramon was accidentally shot by his own guards and presumed dead by the turtles. Zanramon is not heard of again until TMNT (vol. 4) #28, where Michelangelo is informed that Zanramon had survived, and was no longer Prime Leader of the Triceratons: after the Fugitoid's escape, the then-leader lost political capital, and he was quickly deposed by opposing factions.
In the 2003 series, Zanramon was likewise the ruling dictator of the Triceraton Republic seeking the teleportal device to use against the Federation. His troops managed to capture the Fugitoid and the Turtles, but they eventually escaped with the aid of Traximus. Zanramon was taken hostage, long enough for the Turtles to shanghai his personal cruiser to make their getaway. When the Turtles and the Fugitoid were cornered by both the Federation and the Republic, they were pulled out by a timely teleportation, courtesy of the Utroms.
Eventually, the Triceratons managed to find trace the Fugitoid to Earth and invaded the planet in hopes of capturing him. The Triceraton takeover was swift, and Zanramon addressed the leaders of the world to bring the Triceratons the Fugitoid. When Donatello was captured and brought before Zanramon for questioning, he was barely able to convince the Triceraton leader that the Fugitoid was not on Earth, convincing him to break off the invasion. Unfortunately, just as the Triceratons pulled out, Professor Honeycutt returned to Earth to surrender himself to the Triceratons, and once again Zanramon sent his forces down to Earth to capture the Fugitoid.
When the Fugitoid released a virus that stopped the Federation ships cold, Zanramon ordered his ships to open fire on his helpless enemies. His ruthlessness eventually riled Mozar, his military commander, when he ordered him to attack the Tricertion rebels. Mozar refused to carry out that order and allowed Traximus's Triceraton rebellion to overthrow Zanramon. Zanramon was last seen in a cell opposite of his arch-enemy General Blanque, where they stubbornly continued their war - albeit now on a more face-to-face level. In the video game Teenage Mutant Ninja Turtles 3: Mutant Nightmare Zanramon (piloting the Trigolem) was a boss in there.