Before James Mangold was hired to direct The Wolverine, the solo X-Men movie was set to be helmed by Black Swan and Requiem For a Dream director Darren Aronofsky. The version of The Wolverine that Aronofosky was working on was quite different from what ended up in theaters in 2013, and would have had implications that changed the 2017 sequel Logan as well.
Before X-Men: Origins - Wolverine was even released, there were already plans in place to make a sequel set in Japan, which would be based on a limited comic series by Chris Claremont and Frank Miller. One of Origins' post-credits scenes established Logan as being in Japan, directly setting up the sequel. Christopher McQuarrie (Mission: Impossible - Fallout) was hired to write the script in August 2009, and Darren Aronofsky was confirmed as being attached to direct in October 2010, but stepped away from The Wolverine in March 2011.
After Aronosky's departure, The Wolverine's script was rewritten by Mark Bomback and Scott Frank (McQuarrie went uncredited in the final version of the film). Though the bones of the story that ended up on the big screen were similar to what Aronofsky had been working on, there were some big changes as well.
Why Darren Aronofsky Left The Wolverine
In his March 2011 statement to the press, Aronofsky said that he'd decided not to direct The Wolverine after he realized it would mean being away from his family for up to a year, praising McQuarrie's "terrific" script and expressing regret that he wouldn't get to bring it to the big screen. The director later elaborated on his reasons for quitting in an MTV News podcast. He was going through a divorce from actress Rachel Weisz at the time, and working on The Wolverine would have meant being away from their young son at the worst possible time:
"I loved the script and I thought the film came out great. I just had… it was a hard time in my life... It was complicated. I couldn’t leave New York for that long an amount of time. And, to be honest, the possibility of ‘Noah’ had started to emerge, and here was something I’d been thinking about for years. I was really excited by that."
Noah was the biblical epic starring Russell Crowe and Jennifer Connelly that Aronofsky went on to direct as his next project instead of The Wolverine. In addition to the above reasons for quitting the film, Aronofsky had never been particularly enthusiastic about the comic book movie genre, telling The Reeler in 2006, "I'm not a superhero type of guy." This may have been what drew him to McQuarrie's take on The Wolverine, which wasn't really a superhero type of movie.
How The Wolverine Changed Under James Mangold
McQuarrie's original script for The Wolverine doesn't mention mutants at all, and is much more of a standalone movie than a sequel to any other X-Men movie. For example, the scenes in which Logan is haunted by Jean Grey are not present in McQuarrie's script. In a 2012 interview with Screen Rant, McQuarrie told us that his script, while still being part of the X-Men universe, was set much more in the real world and particularly influenced by Japanese cinema and Spaghetti Westerns:
"Well you know, it was an X-Men movie - it was a Marvel movie - but it existed very much in a real world. And more than anything, I love it for the very fact that - at least in the script I wrote - he was the only mutant in the movie... It was what you'd imagine the Wolverine universe to be under the control of somebody who wrote The Usual Suspects and The Way of the Gun and is a fan of Sergio Leone. It was Kurosawa's Wolverine. There was a real romance to it, there was real humor to it, and a very straightforward sort of plain-faced brutality to it."
In Mangold's version of The Wolverine there are two other mutants besides Logan (and the ghostly Jean Grey): Yukio has precognitive abilities, and Viper has serpent-like attributes that include the ability to secrete venom. In McQuarrie's version of the script, Yukio has no powers and Viper uses chemical compounds, poisoned knives and needles to create her "venom" and fight with it. Wolverine being the only mutant in the movie helps to make him more of a unique and legendary figure - especially at the end of the movie, when he inadvertently becomes the Master of the Black Clan and orders its members to commit seppuku.
How Aronofsky's Wolverine Would've Affected Logan
The most obvious way in which Aronofsky directing The Wolverine would have changed Logan is that Logan would probably never have existed. That is to say, 20th Century Fox almost certainly would have made a third standalone Wolverine movie, with or without Aronofsky returning to the helm. But Logan was co-written by Mangold and The Wolverine screenwriter Scott Frank, both of whom were only brought in after Aronofsky dropped out. Moreover, Fox's faith in Mangold (and it did take faith to green light an R-rated superhero movie in which Logan is becoming a creaky old man) was based on the success of The Wolverine, which was not only a box office hit but also restored shine to the X-Men offshoot franchise after the rough start of X-Men: Origins - Wolverine.
It's doubtful that Aronofsky would have actually returned to direct Logan. Recalling his work on a film adaptation of Frank Miller's Batman comics in the interview with The Reeler, the director explained that it was only ever meant to be a springboard into his real passion project:
"Anytime you do something that doesn’t fit into the studio box, it’s pretty hard. So, when it came up that they wanted me to work on [Batman], I was like, 'Well, I just made a $4 million movie about drugs. Maybe if I take their most valued franchise and tell them I’m interested, they’ll let me make The Fountain.' So, it was kind of like a strategic move. But, I wasn’t really into it... I just really wanted to make The Fountain."
At the time when he was attached to The Wolverine, Aronofsky's big passion project was Noah, and forward momentum on that project was one of the reasons that he left Fox's Marvel movie. If Aronofsky had directed The Wolverine, he would most likely have used it as a springboard to get Noah into production, rather than booking himself in for a superhero sequel and putting off the movie he really wanted to make for another few years.
Had McQuarrie's script for The Wolverine been used, he would likely have been brought back to write a sequel (assuming that The Wolverine was still a success), but there's no telling who might have directed it. While Aronofsky fans may be disappointed that they never got to see his take on the Wolverine-in-Japan movie, his being replaced with Mangold definitely worked out well in the end.