I'm guessing eventually we'll learn why Christopher Eccleston left Doctor Who after its first season, however, I don't think we'll see it until long after he's left this mortal plain.
What happened during his short tenure is up to speculation, and strangely in this day of social media and people selling their souls to make money, its surprising the truth (whether real or not) has ever materialized. A little over a year ago, he made some comments about it, but they're still fairly nebula's:
"I left Doctor Who because I could not get along with the senior people. I left because of politics. I did not see eye-to-eye with them. I didn't agree with the way things were being run. I didn't like the culture that had grown up around the series. So I left, I felt, over a principle."
What exactly caused this riff has never been clearly explained. Some have speculated over the years it had to do with casting of the Doctor himself, that showrunner Russell T Davies wanted Eccleston while the BBC wanted David Tennant (it was well known that he was second choice to play the Doctor back then -and in some ways might explain why Tennant was so quickly signed before it was announced that Eccleston was leaving). Of course, that could be the opposite, but to me, looking back on season one as compared to season two, that first year was terribly dark in tone.
I can guess that the BBC heads thought they were going to get a Doctor Who similar in tone (but more modern take) to TOS. Only what they were getting, instead, was a broody, emo, more alien Doctor who is carrying a load of pain, loss and sadness around the galaxy. Heady stuff for children indeed. But as an actor, being able to explore those themes must've have been one of the reasons that attracted Eccelston in the first place.
So maybe, in the early days of production, the BBC was concerned about the tone of the stories, concerned about the tone of Eccelston's performance and made his life and that of the production team difficult. He spoke at one time about some sort of "bullying" from people on the set, that included directors.
[I]t’s easy to find a job when you’ve got no morals, you’ve got nothing to be compromised, you can go, ‘Yeah, yeah. That doesn’t matter. That director can bully that prop man and I won’t say anything about it’. But then when that director comes to you and says ‘I think you should play it like this’ you’ve surely got to go ‘How can I respect you, when you behave like that?’
And while I loved Tennant as the Doctor, I missed the darker tones of Eccleston's ninth Doctor. I miss the creepy, ominous stories of that era. To me, season one of the revived series matched the story telling of Tom Baker's middle years as the fourth Doctor, when those stories had a real sense of forbidding to them, a darkness that made you wonder if you were indeed watching a kids show, or an adult drama dressed for kids.
In someways, now under Steven Moffat, I think the show is trying to return to that first season style. Sure, Matt Smith's Eleventh Doctor is crazy, funny "mad man with a box." But the stories have an undercurrent, a creepy darkness that elevates the show above the campiness that over took it when showrunner John Nathan Turner turned the later years of TOS into a funhouse of gloss and showmanship, but ultimately a tub of empty calories.
Anyways as the BBC begins preparing to celebrate Doctor Who's 50 anniversary in 2013, he's making it clear that he has no regrets about leaving:
"My conscience is completely clear. I've lived my life, particularly my working life, on the basis that I have to be able to look at myself in the mirror about the way I behave. It wasn't a bold move, it was an entirely natural one. I'm hugely grateful to the children who to this day come up and talk to me about the show."
Which is a not so subtle comment that he wants nothing to do with whatever is going to happen.
For me, I guess, I can understand his desires. It's a shame, just the same.
In the end, I guess someday we'll learn the full story. But until he sits down and writes about, we still have that wonderful first season of Eccleston as the ninth Doctor. Sure, not all the stories worked, but he shined in every episode, bringing such a totally different take on the Time Lord. I relish his time there, when the stories and the character returned to the more alien take that started the franchise.