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X-Men: The Chaos Engine Trilogy, a trilogy of X-Men novels by Steven A. Roman (later an author for Short Trips), concerned the X-Men being sent by Roma, Merlyn's daughter and Supreme Majestrix of the Omniverse, to investigate distortions to Earth-616 caused by Doctor Doom reshaping it with a, and in the next books and the Red Skull. As such it featured extensive use of the Captain Britain Corps and other Marvel UK-related concepts.

More relevantly, it also features the character of the "Chief Physician" of the, a doctor at the extratemporal base of , who is clearly intended to be the Seventh Doctor. He is described as "a smallish, wide-eyed man wearing green surgical scrubs and gray, checkered pants, his voice tinged with an unmistakable Scottish burr." The Chief Physician is an expert in many types of science and technology, speaks in meter, wit and riddles, and no one can remember his name so he is most commonly referred to as "Doctor".

In, the Chief Physician first appears to examine the incapacitated Doctor Doom, who has been fused with his counterpart due to a faulty. It is explained that the role of Chief Physician was originally going to go to Henry Stanton, a minor antagonist in the novels, but Roma convinced her father (Merlyn) to instead employ her choice from "some godforsaken corner of the Omniverse". The Doctor also recognizes and addresses her as "Special Executive", a title she claims she has not held since she worked for the Dimensional Development Court.

The Doctor successfully separates Doctor Doom from his counterpart using a "multiphasic crystal accelerator", an invention of Merlyn's which creates minor space-time ripples. However, while Roma waits for the X-Men to return from the world now fashioned by Magneto, Doom convinces Dr. Stanton, who is bitter at the current Chief Physician having taken his role, to free and assist him. Doom's weapons do not work due to the citadel being in a "state of temporal grace", however he realises as what is technically a medical device, he can utilise the crystal accelerator to create a "dimensional destabilizer" to take over the citadel and then the Omniverse.

The Doctor encounters Doom and plays the fool until he determines Doom's plan, upon which he warns him that it will likely end up sending everyone in the Citadel into the vortex. Realising the Doctor's intelligence, Doom offers him a position by his side, to which he responds that he has "never been very good at taking orders from dictators" and has encountered "far greater megalomaniacs" than Doom. For this response, Doctor Doom uses the dimensional destabilizer to open a space/time rift inside the Doctor's chest, splitting him in two and pulling him into the vortex. What happens to him after this is not explained.

However, the Chief Physician makes a reappearance at the end of the. During the climax, the Red Skull, in possession of the Cosmic Cube and the captured X-Men, learns of the Starlight Citadel, and battles Doctor Doom for control of it. This ends with the Skull falling into the void, and Doctor Doom being detained. During the battle, Captain UK also falls into the void, but after  restores dimension 616, Captain UK is returned safely. She arrives in the company of a tall man with "an enormous bush of brown curls", "a baggy gray suit and overcoat", and "a wide-brimmed brown hat", i.e. the Fourth Doctor. The Doctor explains he was on his way there when he found Captain UK adrift in the vortex. When Saturnyne does not recognize him as the Chief Physician, he recalls their earlier meeting (as the Seventh Doctor) and says "I'm not just the man I used to be... or will be..." The Doctor then returns to his role as Chief Physician and assists Roma in rebuilding the body, who was killed in the first book before finding himself in the body of his counterpart of the Red Skull's Earth. Before the novel ends, he offers Roma a jelly baby.

Also of note to Doctor Who in the trilogy is the description of the Starlight Citadel as "dimensionally transcendental", and is protected by "transduction barriers". Additionally, at one point, Psylocke thinks the Cosmic Cube seems "like something out of Star Trek, or Doctor Who, indicating that the Doctor is fictional on Earth-616.