He eludes Blanque with the help of a friendly alien known as one of theVarlesh. The crab-like creature hid the droid under his massive shell as Blanque's Federats raced straight past none the wiser. After their passing of this valley of telepathic crustaceans, Honeycutt decides to continue to evade capture. Thanking his new friend for the temporary sanctuary Fugitoid escapes into the city but gets cornered by more Federats. By happenstance, the fourTurtles teleported onto his scene and had to defend themselves. Honeycutt directed them to safety as he explains his predicament. The Turtles ask him to build his teleportal and use it to bring them and it to Earth where the Federation would not find him. But before they could leave D'Hoonib, Triceratons "robonapped" Honeycutt and took him to their homeworlds. There, Prime Leader Zanramonpromised Honeycutt that they would use his invention for peace but the Turtles ending up captured drops the fake face. Honeycutt finds difficulty and creating his device that his people's enemy intends to wipe out. Zanramon decides to give Honeycutt further persuasion by placing the Turtles in the Games but they escape and hold the Prime Leader hostage. They escape the homeworld on Zanramon's personal cruiser and outrun the Triceratons, only to run into a Federation fleet. By causing both sides to clash with each other, the Turtles and Honeycutt build the teleportal on a planetoid. But both sides attack and the teleportal doesn't work. They are forced to use the last resort: fry Honeycutt's memory. But a transmat from Earth brings them back. While conversing with the Utroms on their techno-organic devices, the Turtles and their master Splinter were learning Utrom history. Unfortunately, the military and the Foot Clan shatter their peace. Honeycutt plays a major role in the Utroms' escape by mimicking the Shredder's voice to overrideBaxter Stockman's voice commands. The Utrom Mortu offers Honeycutt asylum on their homeworld, which the professor accepts.
Unfortunately, their transport to Earth brought the Triceratons, who attack the planet. Seeing the carnage he caused, Honeycutt returned to Earth to surrender himself, just as the Triceratons leave the planet after finding no trace of his positronic signature. He calls to them to capture him, but the Turtles refuse to let their friend's knowledge be misused. They split Honeycutt into pieces, diverting the Triceratons while Donatello erases his signature. Unfortunately, the Earth Protection Force captures them and turns Honeycutt over to Blanque, who attached his body to wires. But all trace of the teleportal is erased and Honeycutt uplinks his mind to the Federation fleet above and broadcasted his message all around Earth. He then dies. The Turtles then grant him a space funeral, sending his body into space.
However, unknown to everyone, while trying to erase his positronic signature, Honeycutt's memories and brainwaves were uploaded to Earth's satellites. He tried to contact the Turtles but all what Donatello got was an irritating ringer. He eventually managed to translate the ringers to his PDA, which Honeycutt inhabited. But due to lack of data space, he had to delete non-essential information, such as Mikey. He helped the Turtles andKarai disable a Triceraton gravity generator which held Beijing in the sky and carefully lower it to the ground. But he accidentally placed it the wrong way.
With Leatherhead's help, Honeycutt was able to create a new, but (since Earth technology was still too primitive) rather crude robot body and subsequently assisted the Turtles against Agent Bishop and the Shredder. Back in the PDA, he initiated a lockdown on the Shredder's mansion and was prepared to take complete control of his ship, the Shredder' in his new exo-suit, slash him from the console, but due to a lucky break from Bishop's missiles, they forced the Shredder outside of the core. Since the Shredder was getting the better of them, the Turtles asked Honeycutt to overload the core. Luckily, the Utroms retrieved them and had Honeycutt transferred back to his body. He was present at Ch'rell's trial and presumably stayed with the Utroms for a while.
The Fugitoid's body can be seen in Cody's collection hall. It is unknown if he was still alive at this point.
Honeycutt later returned to Earth to act as the minister for Casey Jones and April O'Neil's wedding.
A message from Professor Honeycutt to the Utrom High Council: My dear friends, by the time you receive this, I shall be gone. This morning, a sub-space fueling device, planted on the Earth, alerted me to the planet's imminent fate. As you know, both the Triceratons and the Federation want the plans for the Teleportal device, so that they may use it to further their war of annihilation against each other. They will destroy the Earth in their hunt for me. I have calculated and recalculated the probabilities and there is only one sure solution: I must erase all information pertaining to the Teleportal and then surrender myself to the enemy. I know the risks are high and there is a 95.6% certainty that I will not return, but I beseech you, do not try to stop me. For it is as they say: Greater Love has no robot than this. That he must lay down his RAM for his friends.
- This episode marks the first reappearance of Mortu and his people since Secret Origins. They are seen in the beginning when Professor Honeycutt reveal in a message that he has teleported himself back to Earth in reason to end the war between Triceratons and the humans, leaving Mortu and his friends in deep sorrow.