Due to his decidedly short screen time, the Sixth Doctor appeared with only two companions, most notably the American college student Peri Brown (Nicola Bryant), who had travelled with his previous incarnation, before being briefly joined by Mel Bush (Bonnie Langford), a computer technician from his future who he had yet to actually meet during his trial.

Alongside "The Nightmare Fair", "The Ultimate Evil", "Mission to Magnus", "Yellow Fever and How to Cure It", the remaining stories were still under development in a 25-minute episode format after the season was postponed.

There are also novels and audio plays featuring the Sixth Doctor, and the character has been visually referenced several times in the revived 2000s production of the show.

In The Marian Conspiracy (2000), a new companion was introduced - Dr. Evelyn Smythe, a middle-aged history lecturer on the verge of compulsory retirement whose sharp tongue and unwillingness to tolerate the Doctor's attitude steadily taught him to rein in his more unkind tendencies.

In addition, beginning with the webcast Real Time (2003), his costume was revised into a monochromatic blue variant, displayed on many audio stories' covers since then.

The audios in particular depict a range of people joining the Doctor's travels, including history lecturer Evelyn Smythe, "Edwardian adventuress" Charley Pollard (a former companion of the Eighth Doctor who is rescued by the Sixth as part of a temporal paradox), supermarket check-out girl Flip Jackson, and WREN code-breaker Constance Clarke.

The Doctor eventually encounters Mel accidentally during the events of the BBC Books novel Business Unusual and accepts his fate once she stows away in the TARDIS.

The Virgin New Adventures series suggests that the Seventh Doctor somehow deliberately killed the Sixth, because he could not become the masterplanner and manipulator that his next incarnation became, due to his fear of becoming the Valeyard.

[6] The Sixth Doctor wears a scarlet plaid frock coat, with green patchwork, and yellow and pink lapels over a white shirt with crimson question marks embroidered in the collar (a feature of the programme since 1980), a waistcoat with a fob watch, a large tie, yellow trousers with black stripes, and emerald green ankle boots with royal orange spats.

The "future" version of the Sixth Doctor seen aboard the Hyperion III (The Trial of a Time Lord) wore a stripey waistcoat and a yellow cravat, speckled with black stars.

[8] During Baker's run in the stage play Doctor Who – The Ultimate Adventure, the original frock coat was replaced by a similar one with a scarlet, blue and purple colour scheme.

First used in the webcast Real Time, due to the limited availability of colours in the type of animation used, it has appeared subsequently on covers of audio dramas from Big Finish Productions.

In the Big Finish audio Criss-Cross, the Doctor is depicted on the cover as wearing a brown-and-scarlet tweed jacket and waistcoat with a blue-and-white striped shirt, along with a navy blue bow tie with crimson spots, while acting undercover in Bletchley Park in 1944 after the TARDIS is rendered inoperable by a strange signal.

Penguin Fiftieth Anniversary eBook novellas The Sixth Doctor was featured in a number of acclaimed comic strips drawn by John Ridgway.

Colin Baker himself wrote a comic book special called The Age of Chaos in which the Sixth Doctor and Frobisher visit an older version of Peri.

In 2024, Callum Jones of Screen Rant wrote that Colin Baker's tenure as the Sixth Doctor was "very much a waste of both the actor's talents and the character's potential".

Ultimately, Jones suggested that it was the producer's "poor handling" of the Sixth Doctor's character that resulted in the series' decline in popularity and eventual axing in 1989.