Note: The following article is relatively spoiler free for Logan.
While Logan certainly tied up a lot of loose ends for Wolverine and the X-Men, but there were still a lot of unanswered questions by the end of the film. One such question was what was causing Logan's "sickness?"
From the previous films and comics, we know that Wolverine can regenerate and heal himself in a matter of moments, yet in Logan it appeared as though he was not able to heal himself at nearly his usual speed, if at all. So what the hell happened to him?
The film never goes into too much detail about his illness. It alludes around the fact that he is possibly dying from #Adamantium poisoning, which occurred in the comics, but they never go into any detail about it. In fact, the characters seem to purposefully glaze over it in order to avoid explaining whatever the hell is poisoning our favorite X-Man. However, the real answer may actually be in the previous Wolverine film, The Wolverine from 2013...
In The Wolverine, Logan goes through a similar arc as he realizes he is not healing nearly as fast as he used to. In fact, he once again did not want to heal during that film and was ready for death to take him. All of this because he was still recovering from the death of Jean. The similarity between these two films is quite uncanny, now that I think about it.
Any who, in The Wolverine, it is revealed that his healing factor is being slowed down to a parasite placed on his heart by Viper, one of the film's main antagonists. Before the end of the film, though, Wolverine reaches into himself and drags the parasite away from his heart, re-enabling his healing factor.
So How Was It Still Affecting Him In Logan?
After The Wolverine came X-Men: Days of Future Past, which saw Wolverine travelling back in time to stop the apocalypse and all that jazz. In the end, he created a new timeline which he woke up inside of at the end of the film. The trick is, our Logan had no memory of this new timeline after 1973. The memories of the Logan of that time line were wiped out in place of the Logan we have been watching since the original X-Men in 2000.
This is FOX's tricky way of saying that some of what happened in the previous films still happened in the current X-Men timeline (for example, Logan proved that the climax of X-Men featuring the Statue of Liberty still happened), whereas some other parts did not happen. It's extremely confusing, and honestly not entirely well thought out, but I digress.
The main theory here, and one of the few possible solutions to the burning question of Logan's illness, is that during the current X-Men timeline, but before old-timeline's Logan replaced the memories of this-timeline's Logan, Viper still managed to get the parasite onto Wolverine's heart. The catch is that, due to the time-line being different, the events of The Wolverine may not have ended in this timeline the same way it did in the film.
Perhaps the events of that film ended radically different from the movie we know, and Wolverine did not end up getting the parasite out of his heart. This is entirely possible, and probable, considering he still has his metal claws in Logan, which he lost shortly after getting the parasite out of his heart during The Wolverine.
The really tricky part is that Logan would not have realized he still had the parasite in him after he returned in at the end of Days of Future Past. In his memories, he had taken the parasite out, and he would not have been able to ask the Logan of that timeline because he now was the Logan of that timeline, having wiped out all of his memories.
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At some point down the road, Logan likely did realize that the parasite he had ripped out of himself in the other Universe was still inside of him in this Universe. However, this may have been after the decimation of the other mutants, turning Logan back into his old, suicidal self with no aspirations to live, thus no aspirations to get the parasite out of him a second time.
Considering that James Mangold, who directed Logan, also directed The Wolverine, it is entirely possible. He would be able to establish a strong connection between his two films and would be the least likely person to completely abandon his original Wolverine film.
Unfortunately, we will likely not get any confirmation on this until Mangold, or another above-the-line crew member for Logan, comes out and explains exactly what was tearing away at Logan. Until then, this may be the strongest theory we have.
What are your thoughts? Let me know in the comments, and thanks for reading!