- Annihilation Earth, Part 2 - The Ulixes saves the Turtles before the Earth is destroyed.
- Beyond The Known Universe - The Ulixes takes the turtles 6 months back in time.
- The Weird World of Wyrm - The Ulixes receives a mysterious distress signal.
- The Outlaw Armaggon! - The Ulixes is damaged by a vicious bounty hunter.
- Riddle of the Ancient Aeons - The Ulixes is remains in orbit of the planet Xaava-Dal, while the team descend to the planet using the ship's scout ship in order to obtain the first fragment of the Heart of Darkness.
- Journey to the Center of Mikey's Mind - The Ulixes takes the team to a space cantina called Zayford's Cantina, a bar mostly populated by outlaws from throughout the universe with nothing to lose. Later, the Ulixes departs from Zayford's, but is soon unknowingly invaded by the Neutrinos, courtesy of Vrax Belebome.
- The Arena of Carnage - The Ulixes closes in on the Triceraton mothership, where the Turtles then use the scout ship with stealth mode to sneak aboard the mothership, but are immediately captured. Later, Fugitoid remote pilots the shuttle so that he, April and Casey can sneak aboard the ship to save the Turtles and confiscate the first fragment of the Heart of Darkness. They are successful, and retreat with the fragment to the ship and warp off into space.
- The War for Dimension X - The Ulixes remains parked in outer space with April and Casey onboard guarding the first piece of the Black Hole Generator, looking quite angry, while the Turtles and Fugitoid use the scout ship to travel to Dimension X, in hopes that the Utrom Council will reveal to them the locations of the remaining two fragments.
- The Cosmic Ocean - The Ulixes journeys through the Cosmic Ocean of Varuna in order to obtain the second fragment of the Heart of Darkness, where the team is introduced to the Daagon and their supreme ruler Hiidrala, who informs the them that she will hand it over to them if the cosmic monster Cthugga drams them worthy. The ship is later hijacked by Armaggon so he can destroy them and steal the generator fragments to give to Lord Dregg. After obtaining they obtain the second fragment and supposedly defeat Both Dregg and Armaggon, the team then departs the cosmic ocean and sets a course for the very of the known universe to obtain the final fragment of the generator on the lost world of Magdomar before the Triceratons can.
- Trans-Dimensional Turtles - The Ulixes is on course toward the end of the known universe, but along the way, Fugitoid detects a trans-dimensional anomaly centered around the Leo, Donnie, Raph and Mikey, which then teleports the Turtles to the 2D Earth dimension.
- Revenge of the Triceratons - The Triceratons catch up with the Ulixes and surround it with several flagships. Captain Mozar plans to take back the fragments of the Heart of Darkness by force, and so the Triceratons launch a full onslaught on the ship. The team tries to warp away, the Triceratons damage the ships warp engines, preventing them from escaping the system. They then launch the Skeevix Virus to destroy the ship from the inside out. With Fugitoid's robot body deactivated, the Turtles then heads toward a cloud nebula and cloak the ship so the Triceratons couldn't find them. Soon, the Skeevix Virus hatches space gremlins that then try destroying the ships interior maintenance. Eventually, the ships cloak wears off and the Triceratons resume hunting them down. Furious that the virus didn't destroy them, Mozar sends some soldiers aboard the ship to steal the fragments. Once they do, the Triceratons attempt to finish the ship off, but after Donnie repairs Fugitoid's robot body, he is able to power the ship with his fusion core and they're able to warp away, while the Triceratons have successfully obtained the first two fragments. The Ulixes have sustained structural damage on the inside and outside and needs to visit a service station.
Once the ship is fully repaired, the team will continue to obtain the final fragment of the generator before the Triceratons can, then take back the other two fragments and kick their butts.
- The Evil of Dregg - Since their recent fight with the Triceratons, the Ulixes is finishing up repairs from a space service station. With everything repaired, the team then takes off and resumes course toward the end of the known universe, but soon receive an in coming distress signal from Mona Lisa, and the ship then sets a course for Sectoid 1, Lord Dregg's home planet, to rescue Sal Commander.
- The Ever-Burning Fire - The Ulixes finally reaches the lost world of Magdomar, where the team attempts to obtain the final fragment of the Heart of Darkness. The team locates the fragment, but the ships tractor beam is unable to pick it up because it's caught under giant boulders. Before the they can free it manually, Lord Dregg then shows up and shoots down the ship, forcing the Turtles, April and Casey to retrieve on foot, while Fugitoid stays behind to repair the damages. Once he finishes repairs, Fugitoid attempts to grab the fragment with the tractor beam before it falls in the lava. Unfortunately, Dregg then snatches the fragment and brings it to the Triceratons. After failing to retrieve the final fragment, the team then sets a course for the Milky Way Galaxy, so they can return to Earth before history repeats itself and the Triceratons destroy the planet once more.
- Earth's Last Stand - The Ulixes and the Triceraton mothership finally reach the Milky Way Galaxy, and as they get closer to Earth, Fugitoid finally reveals to the team that it wasn't the Kraang who created the Heart of Darkness, it was actually him. Feeling hurt and betrayed, Leo loses all faith in Fugitoid, and attempts to take on the Triceratons head on with the scout ship, which then is destroyed and the faceplate of his space helmet breaks open, causing Leo to lose consciousness. The Triceratons then try to destroy the Ulixes by forcing it to crash into Mars, however, the ship avoids crashing and go to rescue Leo. After they do, they then head to Earth, where history is staying on course when Earth was destroyed the first time. Fugitoid tells the team that he has a plan to destroy the generator and save the Earth at the same time, however, they don't trust him because they believe he'll just keep the generator and destroy the planet himself. Fugitoid then kicks them off his ship and they're plummet down to Earth. Before they hit the ground, Fugitoid use his tractor beam to place them safely down to the ground, and then the Ulixes takes off. The team then arrives to Washington Square where the Heart of Darkness is about to go off once again, right at the moment where Shredder killed Splinter. Fortunately, thanks to Leonardo's verbal warning, Splinter is able to avoid the fatal blow and give Shredder a well-deserved thrashing. After Mozar and the Triceratons retreat to the mothership and the Turtles reunite with Master Splinter, Fugitoid then uses the Ulixes tractor beam to grab the generator and flies toward the Triceraton mothership. At first, the team assumes that Fugitoid will use the generator to destroy the planet, but then Donnie remembers that Fugitoid said the the Heart of Darkness is only vulnerable to a combination of fusion and dark matter, and that the Ulixes uses dark matter and Fugitoid's robot body is powered by a fusion core, and then they discover that Fugitoid is going to sacrifice himself. Despite the team pleading him not to do it, Fugitoid says with his final words that the Turtles, April and Casey are his friends and he loves them all, and finally, the ship explodes, destroying Fugitoid, the Black Hole Generator, the Triceratons and the mothership as well. As the team mourns the loss of their friend, the Ulixes then arrives to Washington Square, because since there are two sets of the Turtles, April and Casey in the alternate timeline, there are also two sets of Fugitoid and the Ulixes. The Turtles, April's and Casey's past selves then board the ship with Fugitoid and the Ulixes flies them off into outer space. Meanwhile, the previous Fugitoid's robot head floats in Earth's orbit with debris from on the generator and the ship, where it then reactivates, indicating that his brain survived to the explosion.
- Ulixes is latin for Ulysses, the Latinised name of Odysseus, a legendary Greek king of Ithaca and the hero of Homer's epic poem the Odyssey.
- Odysseus is renowned for his brilliance, guile, and versatility.
- In a reference to the Fugitoid's voice actor, David Tennant, who played the Doctor in the TV series Doctor Who, in The Weird World of Wyrm the Ulixes is revealed to be much larger inside than it looks from the outside, just like the Doctor's time and spacecraft, the TARDIS.