When the Doctor Who 50th anniversary special was being developed, showrunner Stephen Moffatt approached Christopher Eccleston (who played the Ninth Doctor on the show) about reprising the role in the special. Eccleston, who didn't exactly leave the show on the best of terms, declined and Moffatt revised the story to tell the tale of the "War Doctor" that eventually aired.
While it was assumed that Eccleston declined an appearance early on, newly revealed storyboards from the special show that Nine was included well into the planning stages of the episode. Though the general story remains the same, the version of the special depicted in the storyboards had some notable differences from what eventually appeared on the screen.
The storyboards were revealed by artist Andrew Wildman, who had previously worked on Doctor Who and returned to the show to help out with the early planning of 'Day of the Doctor.' Wildman worked on episodes such as 'Nightmare in Silver,' 'The Time of the Doctor' and 'Dinosaurs on a Spaceship' and has created a book collecting some of his storyboard work to sell to fans at conventions. Work done for 'Day of the Doctor' shows some of the planning that went into it, with Christopher Eccleston's likeness in scenes that featured John Hurt's "War Doctor" in the final version and a little girl appearing before Nine instead of Billie Piper's Rose Tyler.
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In addition to changing the Ninth Doctor to a "lost" regeneration, a few of the storyboarded scenes played out a bit differently than they did in the final version. Jenna Coleman's Clara Oswald popped a wheelie on her motorcycle while heading to the TARDIS, and Nine first travelled through the portal to meet up with David Tennant's Tenth Doctor (and two versions of Queen Elizabeth I) instead of Matt Smith's Eleventh Doctor. The inclusion of two versions of Queen Elizabeth suggests that the overall plot for the episode remained the same, even if some of the details changed.
Wildman described the basics of what was going on when he was involved with the episode to Bleeding Cool:
"There were going to be three Doctors in this one. The current, 11th Doctor and the previous two. Ok, so it didn’t quite work out that way in the end as we all know. Contracts are an odd thing and in the end show runner and writer supreme, Steven Moffat, had to come up with something… slightly different. At my time of working on the show however it was the three ‘modern age’ Doctors and the current assistant, Clara."
Of course, if Eccleston had returned for the 50th anniversary special, then things might have played out a bit differently afterward. The "War Doctor" left Eleven with one less regeneration than fans had previously assumed, setting up one of the key points of drama in Smith's final episode. If Eccleston had been in the episode instead of Hurt, Smith's transition to Peter Capaldi's Twelfth Doctor might have played out differently since he wouldn't have been fretting over it being his final regeneration.
Still, it's a shame that Eccleston didn't return to the Doctor Who universe one last time. It would certainly have been interesting to watch Nine arguing with himself over whether he should end the Time War or find another way, and fans who were first introduced to the Doctor through Eccleston would likely have enjoyed seeing their first Doctor back on the screen. At least we can get an idea of what might have been if not for some wibbly-wobbly timey-wimey contractual details.
Doctor Who will continue with a Christmas special in December 2016. Season 10 is slated to air in 2017.