The Doctor's reality (Scream of the Shalka)

In one version of reality, the Ninth Doctor was accompanied in the TARDIS by the Master, who by that point inhabited an android body. The Doctor fought the Shalka with Alison Cheney, who joined him in the TARDIS. (WC: Scream of the Shalka, PROSE: The Feast of the Stone)

Relation to other realities
In one line of the Eighth Doctor's life, the Master, after falling into the Eye of Harmony, (TV: Doctor Who) remained trapped within the Doctor's TARDIS. (PROSE: The Eight Doctors, Sometime Never..., The Deadstone Memorial, The Gallifrey Chronicles)

The Eighth Doctor looked into a Tomorrow Window and asked to see his future. One of the possible ninth incarnations of the Doctor was seen sucking on an asthma inhaler and resembled an aristocrat with a high forehead and shallow-sunken eyes. (PROSE: The Tomorrow Windows) When examining the Doctor's timeline, Marnal exclaimed to Rachel that the Doctor had "three ninth incarnations". (PROSE: The Gallifrey Chronicles)

Daughter of Mine was visited several times by an incarnation of the Doctor she described as a "tall white aristocrat". (AUDIO: Shadow of a Doubt)