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In the Spring 1983 issue of Bricks 'n Pieces magazine, Bill was renamed to Captain Indigo, and became the star of a comic series of the same name. The comic series continued through each magazine issue until the Spring 1989 issue, where the third and final story arc was concluded. Mary also appeared in the Captain Indigo comic series, under the name Lieutenant Polka-Dot. The art style and character design of the Captain Indigo comics also changed throughout the six year run, with Indigo's pants occasionally changing colour to white, light grey and eventually blue, and both Indigo and Mary's skin being flesh toned instead of yellow when the comics shifted from black and white line art to full colour.
In the first story, Indigo and Polka-Dot are sent out to investigate a UFO, and are sent back in time to retrieve a magical jewel by the aliens controlling it. The jewel has fallen into the hands of the Black Knight and a wizard, and Indigo and Polka team up with the Crusaders to defeat them and use the jewel to return to their original time period.
In the second story, the duo are sent to a LEGOLAND town, only to be arrested by android police officers. They find that the androids have overtaken the town and imprisoned the real police officers, and after a car chase with the androids, find a robotic city where the androids were created. Inside one of the buildings they encounter Tobor Rekam, a robotic knight, who is the creator of the police robots. Tobor reveals he has created a robotic version of Indigo, which Indigo fights and defeats. Polka-Dot then shuts down the assembly line, and Indigo captures Tobor.
In the third and final story, Indigo and Polka-Dot are accidentally sent back in time by their robot dog T42, where they meet Robin Hood. Robin Hood tells the two adventurers that the Sheriff of Nottingham had been stealing any loot he can get his hands on, so Indigo and Polka-Dot team up with Robin Hood to set a trap for the Sheriff. Once the Sheriff sees Indigo, he reveals himself to be Garth Raider, a space villain Indigo once shot down in a battle with the Stardefender 200. Garth is about to kill Indigo with a sword, when Robin Hood knocks him out with a heavy stick. The Sheriff is caught, and the story ends.