In a town on the planet Manda, Imperial stormtroopers search for a fugitive. Mungo Baobab, R2-D2 and C-3PO wait for Krox inside a cantina. Threepio thinks this place is unsafe and is startled by a two–headed humanoid man. Mungo reassures him it is Krox.
Mungo asks if Krox has what he wants and reminds him about their deal. Krox has been on the run from the Empire and is determined to settle their deal. In return for a large coin, Krox passes Mungo a map to the Roon system. R2-D2 activates a jukebox and dances to the tune, much to C-3PO's annoyance.
When stormtroopers enter the cantina, Krox runs off. Mungo thinks they should stay calm and hope for the stormtroopers to pass over them. However, the stormtroopers recognize Mungo and tell him that he is under arrest in the name of the Emperor. Artoo uses the jukebox to jam the stormtroopers' audio amplifiers so he, Threepio and Mungo can escape. One of the stormtroopers destroys the jukebox with his blaster staff. The lead stormtroopers tells his men that the Emperor wants the map.
Mungo and the droids escape on a green landspeeder and head to the Baobab Archives, where R2-D2 plays a hologram of the map. While Mungo reads the holographic map, C-3PO explains that the planet Roon is hidden in a dust cloud known as The Cloak of the Sith. Mungo plans to follow the Rainbow comets to find a safe path through the Cloak of the Sith to the Room system. C-3PO proposes consulting an Archivist droid but mistakes a statue for the droid.
Alarmed by the statue, C-3PO crashes into a stack of datacards and bumps into the archivist droid. Consulting the map, Mungo and the droids find the astrogation coordinates for the rainbow comets. He tells R2-D2 to record them while C-3PO argues with the archivist droid. C-3PO tells Mungo that he has found the archivist but R2-D2 says he has already found it. Mungo tells the droids they are ready to go.
C-3PO advises Mungo to double-check with the archivist droid and asks why is the Roon system so important. Mungo explains that this expedition will allow him to open the first trade route for Roonstones. C-3PO is hesitant about joining another space voyage but R2-D2 pulls him along. The trio ascend up a turbolift that opens up onto the floor.
Meanwhile, the Imperials, under the direction of Admiral Terrinald Screed, are exploring the Cloak of the Sith with probe droids to see if there are any planets there to conquer. The probe droid returns with a gift of Roonstones and a message from Governor Koong of Tawntoom province on Roon. Koong welcomes Admiral Screed and seeks to form an alliance with the Empire, presenting him with the Roonstones. When Screed says that the Empire will decide how they will deal with Roon, Koong tells him that probe droid contains the coordinates. Eager to acquire more Roonstones, Koong orders his crew to set a course for Roon.
Mungo and the droids follow a rainbow comet through the asteroid field. C-3PO grumbles about space travel but hopes the Roon system will be painful. R2-D2 beeps a disagreement in binary. Mungo hopes to use the Roonstones to save his father's merchant fleet from ruin. Threepio says he is a bad feeling about this. Mungo thinks the protocol droid is being pessimistic.
Mungo sights the Roon Comets and uses them to guide the ship through the asteroid field towards the Roon system. R2-D2 pilots the ship. Despite his efforts, they are hit by an asteroid, causing the ship's stabilizers to break down. C-3PO for his over-confidence as the ship descends into a radioactive ion cloud. Mungo manages to save them by firing the aft stabilizers into the cloud, allowing them to regain control of the ship. R2-D2 also adjusts the stabilizers so that they can get back on the comet's tail. C-3PO is pessimistic but Mungo is upbeat.
Riding the comet's tail, Mungo and Artoo take the ship towards a planetary system within the dust cloud. Mungo hopes to see new worlds and exploit their wonders. However, they instead encounter a giant space station called the New Umboo Lightstation. Their ship is drawn into the space station by a tractor beam.
After disembarking, they are greeted by Governor Koong and his entourage, who apologizes for the tractor beam. He explains that they wanted them to dock without any trouble. Koong mistakes them for Imperial emissaries. Realizing the situation, Mungo claims that they are Imperial observers. Gaff, Koong's aide-de-camp, tries to warn the Governor that Mungo and his droids are not Imperial emissaries but Koong brushes aside his concerns.
Koong takes them on a tour of the station using a grav-cab. They travel through a series of tunnels. C-3PO is disoriented during the journey. Koong shows the guests his gates of Nergon-14, an explosive element sought by many interested parties. Koong also shows Mungo and the droids several captive Mupples within a glass chamber, which he describes as a prized delicacy. C-3PO warns Mungo that Roong and his entourage are pirates.
Meanwhile, R2-D2 inspects the Mupples but one of them grabs him with its tendrils, causing him to fall. Gaff tells R2-D2 to web careful. Mungo agrees with C-3PO but warns that they should not give themselves away. Roong's armored enforcers bring a prisoner named Noop Yeldarb, who used to run the Umboo Lightstation before Koong shut it down and took him captive. A defiant Noop warns that the Empire doesn't rule the Cloak of the Sith region yet.
Shortly later, Admiral Screed arrives aboard a Lambda-class shuttle, blowing Mungo and the droids' cover. They flee into the space station, initially evading Screed and his stormtroopers. The two also avoid a Welding Beetle and a Snic 2-4-2. Mungo reaches a dead end where he is cornered by Gaff, who bests him in combat. Following an argument, C-3PO and R2-D2 head a certain direction but are blocked by stormtroopers, who use their blaster staves to shut down the droids.
The stormtroopers deliver the droids to Admiral Screed. Gaff delivers the unconscious Mungo to Roong and Screed. Screed identifies Mungo Baobab as a representative from the Baobab Merchant Fleet and a fugitive from the Emperor. An apologetic Roong offers Mungo as a gift to the Empire. Screed orders that Mungbo be thrown into a cage with the Mupples.
Gaff reactivates the droids. Screed allows Roong to keep R2-D2 but he orders that C-3PO be reprogrammed. Meanwhile, Noop advises Mungo to handle the Mupples by whistling to them. Knowing that Mungo is opposed to Roong, Noop introduces himself to Mungo. C-3PO is harnessed to the reprogramming machine. Gaff asks C-3PO to suggest a new name to go with his new behavioral circuitry matrix. Threepio initially considers but calls Mungo and R2-D2 for help. R2-D2 struggles against a harness and squeals. Mungo blames himself for landing him and the droids in trouble.
Screed is not impressed with Roong's pirating operation. Roong explains that ever since Gaff shut down the old Umboo Lightstation on his orders, he explains that they have been luring trade ships to destruction with false beacons. Roong hopes to acquire the wealth of the Roong system for himself. Screed reminds him that this plunder belongs to the Empire. C-3PO calls for help. Mungo asks Noop for solutions. Noop points out that they are trapped in their cages.
While pulling a sled, Artoo pretends to blow a circuit and escapes under the cover of smoke, freeing Mungo and Noop by tricking Gaff into firing at the mechanisms holding the energy field within their cages. While R2-D2 leads the stormtroopers and Gaff on a chase, Mungo and Noop rescue Threepio and escape. The stormtroopers open fire on them, causing several crates of Nergon-14 to fall. As the volatile cargo exploits, Gaff warns the stormtroopers not to let the boxes fall on the engines.
R2-D2 pulls a sled carrying Mungo, Noop, and the Mupples towards a tunnel leading to the hangar. While attempting to pursue the fugitives, the stormtroopers allow several crates of Nergon-14 to fall on the engines. This causes the Lightstation's engines to break down, causing the station to drift into the asteroid belt.
Inside the hangar, Mungo throws a barrel into the path of the stormtroopers, causing them to trip on the fuel. Roong tries to reassure Screed that his men will have the situation under control. Gaff advises them to abandon ship. Screed is displeased with Roong's "salvaging" operation. Roong claims it is a minor setback. The Imperials and pirates escape, believing that Baobab and the others were in the station when it exploded.
Mungo and company flee aboard Koong's ship before the station crashes into an asteroid and explodes. Mungo reassures the droids and Noop that even though the pirates have escaped, they have destroyed their operation. The Mupples take a liking to C-3PO and R2-D2. Angered at Governor Koong's incompetence, Admiral Screed throws him and Gaff into the brig. Koong warns that he won't find the Roonstones without him.
Meanwhile, Noop thanks for Mungo and the droids for restoring him to the Umboo Lightstation. Mungo asks for Noop's help in finding the location of the Roon system since they are unable to travel back to Manda. Noop shows them the way to the Roon system. An upbeat Mungo vows to establish a route for the Baobab Merchant Fleet. C-3PO is pessimistic but complies with his master's orders to get the astrogation charts. He is buried under a pile of Mupples.
"Tail of the Roon Comets" was released on DVD in 2004 as part of the Treasure of the Hidden Planet feature film. It was adapted into the children's storybook entitled Escape from the Monster Ship: A Droid Adventure. The Star Wars series' trademark line of "I have a bad feeling about this" is spoken by C-3PO in the episode.
The Mupple species that appears in this episode appears to resemble the Tribble species from the Star Trek original series episode "The Trouble with Tribbles." Additionally, the scene in which the Mupples appear seems to be an homage to the final scene of that episode.
When the pirates prepare to re-program C-3PO, they ask him if he has any preference as to his new name. C-3PO replies "Well, I've always been partial to Anthon—oh dear, what I am saying?" This is a reference to Anthony Daniels, the actor who voices C-3PO in the series, and plays him in the films.