The crew learn to use their ship recreated by the Thermians, using luck and memories from old shows. When they return from defeating a rock monster on a mining planet (to pick up a part to power the ship), they realise that the evil alligator alien Sarris has beamed aboard and overpowered the good guys. He is torturing poor Mathesar, and makes Nesmith explain that he was "lying" and is just a TV actor - breaking his heart.
The crew are led away while the other Thermians are trapped in a cargo room, being slowly starved of oxygen. Staging a fight with Alexander Dane (Alan Rickman), they defeat the guards and send them out an air-lock. Nesmith divides his team - and tells the pilot to get some driving practice in.
Nesmith realises his radio was switched with Brandon's toy (Justin Long, the dejected fan from before), and contacts him for advice to move around the ship and power it back up.
Fred Kwan (Monk from TV) has an idea to get the bad guys out of the bridge, so they can free the captive Thermians who are suffocating. He beams the rock monster on board. The monster smashes up the place and chases the enemy out another air-lock. Fred gets into the bridge and unlocks the door.
An enemy soldiers shoots the loyal Thermian who has been helping Alexander, sending the only human in a costume into a rage who overpowers the remaining guards.
The enemy trigger a self destruct on the ship and beam away. With Justin Long's help, Nesmith and Gwen (Sigourney Weaver) stop the countdown with 1 second to spare. They navigate back through the minefield. The enemy ship realise the countdown was stopped and start to pursue - but soon stop when they see that Nesmith is heading straight back towards them.
Nesmith narrowly avoids a collison - but its only then that the evil commander sees a load of landmines in tow behind the other ship - slamming straight into the enemy, obliterating the enemy.
The good guys celebrate. Fred (Monk) enters the command deck - but then transforms into Sarris, who shoots Nesmith and all the crew. Before he dies, Nesmith manages to trigger the mysterious Omega 13 device - sending them 13 seconds back into the past.
This time, Fred/Sarris enters the command deck but Nesmith beats him up. The others step in - but it is Mathesar who renders Sarris unconscious and saves the day. The real Fred enters later, with his new girlfriend Laliari. Nesmith hands control of the ship back to a new captain - Mathesar.
The ship enters through a black hole to return home to earth - but is travelling too fast. The Thermians remain on the ship while the TV crew separate in a bridge section and drop into the atmosphere.
To get back home they need the nerds on earth to light a landing path for them. The ship crashes back down to earth and smashes into the convention centre, still full of fans. The crew exit one by one to a standing ovation.
Sarris is last to exit and raises a weapon - but Nesmith ducks, dives, and shoots him in time. He is vaporized and the crowd go wild.
Later we find out that the series was brought back - Laliari is given a part (credited as actress Jane Doe), and even Guy (Sam Rockwell) is honoured as the new security chief - this time with his surname listed too!