The English actor discussed his departure from the BBC show in front of a largely American audience on Thursday at New York Comic Con.
Asked about his relatively short tenure as the Time Lord (Eccleston was the first one to play the part when the show was revived in 2005), he said he left due to issues in his relationship with the showrunner and the producer.
Specifically, he said three people had led to his decision to leave the series.
“I left only because of those three individuals and the way they were running the show,” Eccleston said, “I loved playing the character.”
While Eccleston’s departure after one season has remained a subject of speculation over the years, the actor has recently become more open about the topic.
“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,” he added on Thursday. “I became the invisible man.”
Eccleston said he was asked to come back for “The Day of the Doctor”, a special episode marking the show’s 50th anniversary in which Matt Smith, David Tennant and John Hurt all appeared, but that he decided not to do so after reading the script.
“When read it, I felt that it was basically myself, Matt and Dave riffing off the fact that we used to be the Doctors,” he said.
“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.”
Eccleston said the way his departure from the show was portrayed in the media caused him to temporarily lose confidence as an actor and to get blacklisted from shows.
His confidence, he said, came back when he played John Lennon in Lennon Naked, the 2010 BBC Four biopic dedicated to the musician.
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