While Rose, investigating the Doctor, went to visit a conspiracy theorist named Clive, Mickey was captured by the Nestene Consciousness, which created a living plastic facsimile of him to gather intelligence about the Doctor. Kept a captive by the Nestenes to maintain the duplicate, he was overwhelmed by the revelation that alien life existed and was in a state of paralysed panic throughout most of the Doctor and Rose's final confrontation with the Nestenes.

Mickey's initial cowardice did not impress the Doctor, and when he offered to take on Rose as his newest companion, he pointedly said that Mickey was not invited. While mere days passed for Rose in the TARDIS, a year had passed in London when she returned in Aliens of London. In the interim she had been declared missing. Mickey was suspected of Rose's murder and interviewed on five occasions but was not arrested due to lack of evidence. Mickey had also spent the year unearthing information about the Doctor and waiting for Rose to return, taking over the www.whoisdoctorwho.co.uk website formerly run by Clive (see Doctor Who tie-in websites).

Although still dismissive of Mickey (deliberately calling him "Ricky" and terming him "Mickey the Idiot"), the Doctor had to rely on him when the Doctor and Rose were trapped inside 10 Downing Street during the events of World War Three. Mickey's actions in that story, bravely defending Rose's mother Jackie from the Slitheen and helping end the alien threat, earned him a degree of the Doctor's respect. At the conclusion of the story, the Doctor offered Mickey a place aboard the TARDIS but he declined, asking the Doctor not to tell Rose that he had done so. The Doctor in turn gave Mickey a compact disc containing a computer virus that would wipe out all mention of him on the Internet, but according to his website, Mickey is undecided as to whether to use it.

A younger (around six years old) version of Mickey appeared in the episode Father's Day played by Casey Dyer, where he met the time travelling Rose in 1987, although he was not made aware of the role she would play in his future. The present-day Mickey reappeared in Boom Town, where he told Rose that he had started dating Trisha Delaney, although whether this was true or merely to make Rose jealous and return to him is not certain. Although he bitterly walked away from Rose at the end of that episode, he was willing to help Rose get back to the Doctor in the 2005 series finale The Parting of the Ways.

Noel Clarke returned as Mickey in the 2005 Christmas special, The Christmas Invasion, and has signed up for the 2006 season. According to SFX magazine and the producers' commentary on the DVDs, Mickey will become a regular companion, travelling with the Doctor for at least some of that season