The Ninth Doctor had three on-screen companions during his tenure, the main one being Rose Tyler, who appears in all 13 episodes of Series 1. Adam Mitchell joined the Doctor on his travels at the conclusion of Dalek but was left back on earth after trying to change history. Jack Harkness was a 51st century Time Agent turned conman. He was later killed by the Daleks and then resurrected by Rose with Vortex Energy, although the Doctor was unaware of this and accidently left him behind in 200,000AD.

The Ninth Doctor's relationship with Rose verged on the romantic, with both of them clearly showing that they cared about each other deeply, although both always denied that they were a couple. The Ninth Doctor did kiss Rose with some passion in The Parting of the Ways, although it could be argued that this only was in order to draw out the lethal energy of the time vortex from her body.

In his final adventure, the Doctor discovered that The Dalek Emperor had survived the Time War and had rebuilt the Dalek race. The Doctor sent Rose back to her own time in the TARDIS, before attempting to destroy the Dalek army. However, when she saw more "Bad Wolf" graffiti, she realised it was a message linking her to the events in the future. Managing to open up the heart of the TARDIS, she absorbed the energies of the time vortex, and used it to destroy the Daleks. In order to save Rose from being consumed from within by those energies, the Doctor absorbed the fatal energy himself. However, the damage to his cells caused him to regenerate...