According to
The Independent, Eccleston alleged that his exit from
Doctor Whofollowed a complete breakdown in his working relationship with "three individuals and the way they were running the show"—presumably showrunner Russell T. Davies, and executive producers Julie Gardner and Phil Collinson:
I left only because of those three individuals and the way they were running the show. I loved playing the character. I felt I was going to play the Doctor my way and I wasn't going to get involved with those politics and that wasn't workable, so off I went. I became the invisible man.
Eccleston went on to allege that his exit from
Doctor Who lead to him being blacklisted for acting jobs in the UK, leading to the actor taking roles in the U.S. like
his brief stint on
Heroes. As to why
he turned down Steven Moffat's offer for him to return—despite also praising Moffat's writing for his Doctor in "The Empty Child" and "The Doctor Dances"—alongside Matt Smith and David Tennant for "The Day of the Doctor," Eccleston stated that it was because of the narrative in the script
he was given, combined with the lingering politics that led to his departure in the first place:
When I read it, I felt that it was basically myself, Matt and Dave riffing off the fact that we used to be the Doctors. I personally didn't feel like the narrative was strong enough, particularly for the Ninth Doctor because I'd taken quite a lot of abuse in my own country when I left.
As the show was being celebrated I was being abused in the press and that was hard to take and very confusing. So I looked at it and I thought is this really the way I want to come back and I decided it wasn't. There were other factors, political factors.