Captain Baxter orders the USS Sisyphus to fire on an unidentified ship he assumes is attempting an ambush, only to destroy the Federation medical transport the USS Athena. The consequence of this catastrophic mistake most likely mean court martial for the Sisyphus crew. Rejecting the idea of turning themselves in, Baxter suggests the whole crew venture out for themselves, becoming a ship of renegade space cowboys, but concerns about their longevity on such a series(of actions), and a deep rooted love of Starfleet cause some to object. As a compromise Cmdr Hayes and LtCmdr Watson try to scrape together a fifth Quadrant of the galaxy the Sisyphus can get lost in and explore, placing them beyond Starfleet's reprisal but still doing their work. Meanwhile, Ensign Lorem makes the case the that the crew should strand themselves planetside and wait out their troubles in a cave. Lt. Fassbinder and Counselor Japhy speculate whether Starfleet put Baxter in charge of the Sisyphus with the express intent of him leading the ship to its destruction, an idea that only strengthens Fassbinder's loyalty to Baxter. And privately, Dr. "Foggy McCloud" gives Baxter the shocking news that he,"McCloud," is a spy, and that the parties he reports to will destroy the Sisyphus if for any reason they suspect the ships mission is ending prematurely.
Implausibly, Watson finds a stable wormhole to the Omicron Quadrant(a region he invented by combining bits of the Gamma & Delta Quadrants with some extra-galactic void thrown in) but before the ship can travel through the USS Galaxy arrives to arrest the crew. The USS Galaxy is immediately destroyed, leading the crew confused as to how the Sisyphus could obliterate the much larger and more powerful ship. When they examine their records they discover that both the Athena and the Galaxy were destroyed by a mysterious force, which soon reveals itself when they are hailed by their own doubles: The USS Sisyphus from the so-called Abbaverse, commanded by Captain Fritz Fassbinder.
The Abbaverse ship has been monitoring the USS Sisyphus since secretly surviving their first encounter with Dr "McCloud," permanently fused with their own gaseous doctor, serving as a conflicted spy. They regret allowing this universes' Sisyphus to go free and board the ship with the intent of placing their extraneous First Officer Japhy Whitman in command. During a firefight Alt. Japhy is killed and Captain Baxter is severely wounded, leaving Dr. "McCloud," with his literally divided loyalties, to revives Baxter and makes a heartfelt plea: he has grown to love the crew of the Sisyphus and wants to find a peace. He understands why the Alternate crew of the Sisyphus is so warlike, coming as they do from a society based on Abba, and suggests that reorienting their lives around Journey, which both his sides are really into right now, might guide them to a happier life.
The Alt.Siyphus departs and Captain Baxter announces his plans to go AWOL. By taking sole blame for the destroyed ships he can give the Alt. Sisyphus a chance to start a new life and, more importantly, give his own Sisyphus a chance to continue serving in Starfleet. Lt. Cola refuses to let him escape, saying she's sick of presiding over security failures, but Baxter convinces her that the best way to protect the ship and its crew is to ensure it stays together, which can only be done with Baxter on the run. In closing, Winslow Heffington III, the ships time-traveling helmsman, pops open his umbrella and congratulates the crew. When he first arrived everyone was like a child, but under his care they've grown so much and made him truly proud; now he must continue on his way. He holds out his hand and offers to take Baxter with him on his exciting journeys through time and space. Julius Baxter opts for a shuttlecraft instead.
Wheel in the Sky