The Logo Joke features the X-Men in its pages. Given the films’ generally gritty, realistic approach (this film has a definite Western post-apocalyptic setting), this can come off as ironic. However, Laura’s X-Men comic books display an idealized version of the X-Men, which provides inspiration and hope for her and the other mutant children.
How is gene therapy spread in second-world nations and third-world nations that were not subjected to the modified corn syrup used in the North American market? Gene therapy is more typically spread through common viruses, something that would be fairly straightforward in developing nations with poor public health.
Also gene therapy only needs to happen once, with the effects applying to all the affected individual's descendants.
Laura wears a rainbow shirt after they arrive at the casino. Rainbows represent hope after destruction or dark times, and are a biblical symbol of God's promise not to exterminate the human race again with a flood. This sets her up to represent mutantkind's last hope. Also, it's a nice touch, because the X-Men have always represented minorities, and the rainbow is also a symbol of the LGBTQ+ community.
Johnny Cash's career lasted nearly five decades, from 1954-2003. His cover of Nine Inch Nail's "Hurt" was one of the last songs he did in his life, shortly before his death — which fits quite well with the theme of the film, of going out with a bang. Additionally, who directed the biographical film of Johnny Cash released two years after his death? The same guy who directed this film!
It is revealed in the film that the X-Men have comic books chronicling their adventures (although very loosely, as Logan notes), which seems odd, considering the X-Men never really operated as publicly as, say, the Avengers in the MCU, until one remembers that in X-Men Apocalypse that Charles, having now grown tougher and more militant after his brutal ordeal, probably had the X-Men fight more openly, and considering near the end that all the new members are in more colorful comic-accurate uniforms, it is likely that they gained more media attention as the public noticed their actions.
This film also explains, albeit probably unintentionally, where Wade Wilson's Barakapool toy came from. Logan says that the comics are hardly an accurate representation of the X-Men's real adventures, so it's entirely possible that, when asked for ideas for adventures they could have had, Logan described what he remembered from the old timeline (Barakapool survived Origins, and presumably fought the X-Men at some point).
Not one specific to Logan, but to Wolverine in the X-Men films in general. The in-universe (sorta) reason why Wolverine has never worn the iconic yellow suit in any of the films so far? Well, consider the origins of the suit in the comics — Logan first donned the Wolverine costume when he became a member of Alpha Flight, which was basically the Canadian version of the Avengers; a high-profile team of elite superheroes meant to garner attention and (good) publicity. So, in a sense, Logan was used to operating as a superhero and wearing a classic superhero costume, and that carried forward when he joined the X-Men (who were also accustomed to wearing colorful costumes at the time). In the movies however, Logan was never a member of the Alpha Flight (unless his life took a very different turn in the post-DOFP timeline). He never had reason to present or perceive himself as a 'superhero' before he joined the X-Men. And even the X-Men in this verse don't really dress like or present themselves as 'superheroes' most of the time (though that might change in future X-Men movies set in the new timeline). So it makes sense that Logan would never wear a colorful costume apart from wearing an X-Men uniform when he's operating on behalf of that team.
There's an even more obvious in-universe explanation available if the X-Men comics are indeed loosely based on the lives of real people: the publishers wanted to avoid having to pay any surviving X-Men for using their likenesses! This is the reason why the animated Ghostbusters and Aliens action figures looked nothing like their movie counterparts.
How does Logan have an adamantium bullet? X-Men: Apocalypse shows Logan escaping from Stryker in very different circumstances to those seen in X-Men Origins: Wolverine. Jean gave Logan whatever memories she could find, implying he already had amnesia at that point, which means Stryker never fired the adamantium bullets he had, making it possible for Logan to obtain one later.
Freezing during seizures:
Logan and Laura seem to be among the only people who can actually move when Xavier has one of his seizures, while the Reavers, Caliban, and all of the people in the casino are frozen in place and unable to act. It's the same reason why Logan was the only one able to go back far enough to prevent Trask's assassination in X-Men: Days of Future Past: their Healing Factor allows their minds to "snap back" from trauma, granting them a measure of protection from the telepathic assault. They can't shrug it off with no effect, (as evidenced by both being in visual pain) but it does give them the ability to power through it.
However, even normal people frozen by Charles' seizures still retain use of their eyes — one mook even looks at Wolverine before 'ol Adamantium Claws takes him out. Why? Unlike when Charles froze people intentionally in previous movies and shut down everything, including their thoughts, the seizures seem to target the brain stem and motor cortex, which is why they can't move or, as Caliban mentioned, even breathe. But what controls the movement of the eye? Cranial nerves CN III, IV, and VI, which wouldn't be affected by that. The writers did their homework.
Shane:
Laura quotes Shane in the funeral scene at the end. This is likely only her second funeral, and the first funeral she's ever presided over. She's reciting that scene because she had just recently watched the movie with Charles at the casino hotel, and it's the only thing she knows to say in that environment.
While on the topic of 'Shane,' let's not forget it was one of the first revisionist westerns. Director George Stevens served in the US Army during WW2. He wanted to show the devastating power of a gunshot. So he was one of the first filmmakers to use wires to pull the actors and stuntmen back instead of letting them crumple. In 'Logan,' the violence of a superpowered individual using violence against non-powered and even other powered people is shown in all its unflinching horror.
Why has Logan's healing factor weakened in this film? Adamantium poisoning aside, his body was able to handle this with no problem for several decades, so why now? It makes a lot of sense if you consider that the Westchester incident was so traumatic for Logan that it's caused clinical depression, which in real life can inhibit things like your immune system and healing. Once that started for him, his healing factor wasn't enough to tolerate the poisoning anymore, which likely affected his power even more. This became a viscious cycle where his healing factor continued to weaken as the poisoning progressed, which further worsened his depression, which further weakened his healing.
Eden:
The X-23 kids using Eden as their rendezvous point is more than just a convenient place to hide. They got the coordinates from one of the X-Men comic books, and even if Eden doesn't actually exist as a place, it still represents an idea. To them, the X-Men still represent hope, and using Eden as the base for their escape attempt is an expression of that hope.
It's also a convenient place to hide the coordinates for the kids. If they're captured, the comics are found, but who would think something would be hidden there?
Similar to this gesture is the X-23 kids' act of trimming Logan's beard into his iconic muttonchops while he was recuperating at Eden. When the kids got to meet their childhood hero face-to-face, they were probably not expecting a decrepit, cynical alcoholic with malfunctioning powers. Despite this, they welcome him with open arms and still consider him the Wolverine from their favorite comics, to the point that they want to make him resemble his fictional counterpart. Even though Logan is past his Glory Days, he still represents an age of heroes where mutants were relatively free from persecution. Their kindness inspires Logan to once again become the hero he once was and give them a chance at life free from Transigen.
Funeral:
When Laura buries Logan, she flips the cross-shaped grave marker on its side, making an X. The symbolism is clear; Wolverine died an X-Man, a hero.
Additional brilliance: according to tradition, like his brother St. Peter, St. Andrew did not feel himself worthy of being crucified like Jesus, and requested his cross be re-positioned. How was it positioned? Like an "X". Throughout the movie, both Xavier and Logan express how "unworthy" they are.
Also, X literally marks the spot. What does that signify, usually? Something you treasure.
The use of Johnny Cash's "Hurt" in the trailer. Consider the lyrics. Not only is it perfect for Logan's story, but consider that at this point in his life, the once brilliant mutant mind Professor Xavier has lost his "dream" of mutants and humans co-existing, most of his "children", and two of his best friends, Eric and Raven.
So why did the "medicine" wear off so quickly for Logan? His rejuvenated Healing Factor purged it from his system.
Why was Gabriela so adamant on getting Logan's help instead of just taking Laura and running? She knew his genes were used to create Laura, making him her biological father. Gabriela was trying to reunite Laura with her father. When she realized her father was not only one of the original X-Men but alive, it probably seemed like fate.
It seems kind of jarring to see a child in this day and age (or the future day and age) so amused by a simple coin-op pony, especially an eleven year old (they kind of lose their appeal around age five). That is, until you realize Laura has been raised in captivity and never been allowed to have any sources of entertainment her entire life. To her, that lame mechanical pony is amazing. She demonstrates that same sense of wonderment several times throughout the film, such as her first look at the lights of the city when they arrive at the casino, and later with Nate Munson's music player.
By extension, Laura is actually very immature for her age. Most eleven-year-olds know enough to not push buttons at random in an elevator, mess with car door locks, or shovel their food into their mouths with their hands. The behavior on display is more something you'd expect from a child who was five or six. Then you realize that her mental growth was stunted from her isolated and traumatic upbringing; while she may be able to rip through a group of large, heavily-armed men and operate vehicles, she never actually learned how to act her age in more ways than one.
"This is what it feels like," Wolverine's final words in the movie, can be interpreted in a number of ways. Since they are his dying moments, he might be referring to the fact that of all the plateaus he's experienced and overcome in his life, the reality of his own death is one that has eluded him up until now. Or he could be referring to the fact that Laura is by his side, and for the first time in his long life he knows what it's like to not be alone, and to have someone unselfishly love him as family with no agenda. Perhaps he feels content knowing that after many years of "Being the best at what he does, and what he does isn't very nice," that he fought for an unambiguously good cause and was able to be "nice" for once. Maybe he's nostalgic for the days of his prime when he had impressive killer instincts, and despite being past his prime he managed to prove "he was still the best at what he did". Regardless of its meaning, this is a very poignant moment.
In The Wolverine, Yukio, who has the mutant ability to see the death of anyone, becomes alarmed halfway through the movie when she sees Logan's death, describing it as him being "On his back, there's blood everywhere, holding his heart in his hand". In the movie it is played up that he may die when he performs open heart surgery on himself to remove the little robot that is restricting his powers from working properly. But then he doesn't die (Or at least dies for a second and then is resuscitated by his healing factor). Turns out Yukio was wrong. Or was she? In Logan, he dies lying on his back. There's blood everywhere (Like, LOTS), and he is holding X-23's hand. Even if it isn't what Yukio in-canon saw, it is incredibly poetic. X-23 is Logan's heart. She made him care again. He died holding his heart in his hand. "It's still beating."
Yukio says that Logan wishes for an honorable death, which, according to the above analysis of Logan's final words, he got by fighting for an "unambiguously good cause."
Early on the movie, Logan tells Charles that no mutant has been born in 25 years. Assuming this isn't hyperbole meant to be taken in Broad Strokes,note the children appear to be high school age, which puts the youngest born c.2009, right at 20 years before Logan's setting it creates an apparent Continuity Snarl with X-Men: Days of Future Past, as Logan wakes up in 2023 from the new timeline and sees the school filled with children. However, in X-Men: Apocalypse, Charles tells Raven that he would like to start accepting regular people into his school, so if Charles went through with that, what Logan could have seen were non-powered students when he woke up in the new timeline.
Charles and the timeline:
Despite James Mangold's claims of the movie taking place in the timeline created in Days of Future Past, the Call-Backs are actually towards the events of the original timeline; Charles reminds Logan of his time as a cage fighter and the battle at the Statue of Liberty. A case of History Repeats / You Can't Fight Fate? Not necessarily. Xavier is a telepath, and the ending to DotFP establishes that Logan has no memories of the period between 1973 and 2023, but still retains memories of the previous timeline. So it's most likely that the Xavier of this world retained knowledge of events of the other timeline from when he scanned Logan's mind back in '73, or he learned more about it in 2023. When he's calling out Logan for keeping him in the fallen water tower, Charles is referring to the timeline with events that would actually resonate with Logan.
As an alternative to the above, Xavier's remarks are as a result of his degenerative mental faculties, combined with him losing his grip on his powers. Xavier is confusing his own memories of the current timeline, with Logan's memories of his original timeline. Additionally, due to Xavier using Logan's mental link to the bad future, he was able to communicate with his future self, meaning he may even have gotten a complete map of his original timeline through that.
As the most plausible explanation to the above, Charles is talking about a vision of the motel where Gabriela and Laura stayed through the eyes of one of them, and Logan assumed he was talking about the end of X-Men. The motel has a poster of the Statue of Liberty hanging outside.
Gabriela was wrong or at least inaccurate about the insemination method. The "sperm" explanation was probably just quicker and easier and the exact method was not more important than telling about the abuse and the suicides. Aside from the difficulty of getting actual sperm from X-Men without them noticing, and while the girl who breathes frost is plausibly Iceman's test tube baby, the girl who lifts the forest bed is either Jean's or Storm's, and since the point of making these kids is to duplicate already existing mutant powers, the electric kid is Chris Bradley's. They must have used cells from mutants, probably recovered shortly after a fight, while the DNA was still fresh.
The project's decision about what to try next after the X-23 project was written off as a failure was clear — Laura was the closest they got to the superpowered fighting machine they wanted, so they tried again with the same DNA.
Why cast Elise Neal and Eriq La Salle? Well, both were big stars around 2000. If you saw X-Men as a kid, there's a good chance you'll recognize them, and automatically be more sympathetic. So it hurts more when they die. It even fits with the "end of an era" theme in the film.
During the hotel incident, why didn't Laura just kill all the mercs before they got to Xavier? Because she was in the other room when they came in; notice how they seem to be focused on Charles. By the time Logan makes it all the way upstairs, she's managed to crawl most of the way to Xavier. Logan gets farther because he has a lot more experience working through pain, including Charles' seizures.
One possible explanation for Laura not speaking: she barely interacts with Caliban, Charles of course can hear her thoughts, and Logan just orders her around; once he talks to her and not at her, she actually responds.
Her response to Logan is more or less confirmed by a translation of her Spanish dialogue: When she gives her big rant the first time she speaks, she's utterly laying into him over how he'd been treating her up to that point, and she saw no reason to talk to him because he was being such a dick.
Why is the film the only one of the three Wolverine-centered films to not have the word Wolverine in the title? Because Wolverine can refer to both Logan and Laura (especially as she is Wolverine in the comics now), but this isn't Laura's story yet. She may be the new Wolverine, but there's only one Logan.
Given how little the film series has in common with the comics (made double by the fact that the films are not made by Marvel Studios) it is just as likely that they weren't thinking of Laura becoming the Wolverine at all and was referring more to the fact that Logan has clearly denounced the title. The man that was Wolverine died the same day that the rest of the X-Men did; now there is only Logan, a dying old man taking care of another dying old man.
What Xavier says as he dies, is "Our boat...the Sunseeker". This might seem like a bit of an anticlimactic, almost random thing for him to say at this point. But think about what Xavier's motivation has been throughout the entire series, and what his relationship is with Logan. What he wants — probably largely because he can't have children of his own — is to find surrogate family and protect them. Logan, more than anybody, has been the one he's striven to be a father figure for. Xavier...is a son seeker.
Older Charles is seen regressing into second childhood, and so displays distinct traits from his younger McAvoy self (cursewords, a distinct sense of humor).
Throughout his life, Charles Xavier gives hope to others. His last words, “Our boat, the Sunseeker”, whether he was deluded or sane, are a statement of hope for Logan to keep on going.
The scene where Logan, Laura, and Charles stop at the Munson family's house for dinner shows at the start that Logan is justifiably averse to it and the three of them staying there puts the innocent family at risk from the villains. It is possible that, aside from thinking that they need to keep on moving, that one reason why he thinks they shouldn't do this is because it resembles the scene in X-Men Origins: Wolverine where after escaping the Alkali Lake facility after getting the adamantium procedure and running for a little bit, Logan finds a farm with a nice married couple who allow him to stay for dinner, and because he stayed there they get shot dead by the people pursuing him, with him saying afterwards that they were good, innocent people. He was probably worried a similarly unpleasant fate would end up befalling the family (which, sure enough, is exactly what happens).
The 20th Century Fox Logo Joke of the "X" remaining on the screen after the rest of the logo fades to black is absent in this film. You would assume that is because this is not a proper X-Men film. And then it's revealed that the X-Men were all dead before the events of this film. The "X" Running Gag isn't there not because the X-Men aren't featured. It's because there are no X-Men.
Even though the film takes place in an Alternate Continuity, the events of previous movies still happened in this universe, keeping many of the following examples still relevant for this timeline.
If all the mutants died, then not only did Charles outlive Magneto, but he also outlived his students and his own son, Legion, in addition to his sister. On top of that, his mansion/school for gifted mutants is gone for good. Worse than that; it's entirely possible that Xavier killed them himself during his seizure.
Back in the very first X-Men, Logan said that it hurt every time his claws came out when Rogue asked. If his healing powers have slowed to the point that he now scars, how painful must it be to bring out the claws now? Extremely painful, to the point where he has trouble fully extending them sometimes. Even worse, the holes in his knuckles where they extend from have gotten infected and occasionally leak blood and pus.
The Westchester incident:
Logan appointed himself as Xavier's caretaker after Xavier's seizure/epileptic fit destroyed the School for Gifted Youngsters. Given that Xavier's brain was classified as a WMD, some form of authority must have been coming for him on the very same day, so Logan would have to act quickly. Now remember that at the end of X-Men: Days of Future Past, Logan had the position of history teacher. Logan was in the building when the Xavier-Bomb went off.
Keep in mind that we never actually see the incident, making it all the more tragic and horrifying. Imagine you're just going about your normal day when all of a sudden you and everyone else in the vicinity can't move or breathe. Once it's over, you go around to check on all of your friends, those you consider family, only to find half, if not all, of them dead. No wonder Logan's so messed up in this movie.
If the several X-Men that were killed consisted of the same people seen near the end of X-Men: Days of Future Past, it is probably safe to say that Kitty, Storm, Colossus, Cyclops (again), Beast, Bobby, and Rogue were among the victims.
Caliban states early in the movie that he can't breathe during Xavier's seizure. That one lasted less than a minute. When he has another attack at the hotel, Logan has to go from just inside the lobby and up fourteen flights in the elevator before forcing his way into their room. This takes several minutes of screen time, so who knows how long all those people went with limited to no oxygen, fully aware of their inability to draw a breath.
When you compare Laura's behavior for a good portion of the film with X-24's personality, it becomes frighteningly clear that had it not been for Logan and Xavier, she would have probably wound up turning into something not entirely dissimilar. While she probably wouldn't have been anywhere near as mindlessly bloodthirsty, her predatory aggression, violent reactions to anything that could even remotely be perceived as a threat, and overall very animal-like demeanor and mannerisms are all right in line with X-24.
Gabriela's panicked attempts to defuse the situation with the motel owner over Laura's carelessness with the plastic ball she was playing with takes on a terrifying new meaning after witnessing what happens in the convenience store later on: she wasn't trying to prevent a minor scuffle, she was trying to keep Laura from seeing a threat and gutting the woman like a fish, which was all but guaranteed to happen had the woman pushed the issue.
If Logan's original plan to buy the Sunseeker and live out the rest of his days caring for Charles at sea went through, there's a high chance that Logan would outlive Charles. Now remember why Logan has an adamantium bullet.
The film implies that Xavier was mentally communicating with Laura before Logan meets Gabriela at the funeral. What would happen to Laura if Charles had suffered a seizure while they were communicating? Or worse, what would Laura have done to anyone who was in the same room as her while it happened?
During Xavier's funeral, Logan looks down at Laura holding his hand for a brief moment before ripping it away and returning to the truck. When it fails to start, he goes ballistic and starts beating it with a shovel. But what would have happened if he had successfully started it? From the look he gives Laura, it appears he was blaming her for Xavier's death, and may very well have intended to abandon her there. He may have come around after cooling down, but he would still be leaving her behind alone, barely able to look after herself, and with the Reavers still hot on their heels.
It gets worse if you read a translation of her first rant in Spanish. Laura is completely aware that Logan had already tried to abandon her.
We learn of two Transigen projects to turn mutants into weapons, following up on the Weapon X project of the early-1980s: X-23, and X-24. The X-23 project resulted in the births of several mutant children, including Laura, while X-24 is a direct clone of Logan himself. Presumably, that means there's also an X-1 through X-22. That are still out there. That, or they were failed projects (which is likely considering that they would have stopped at the first success) like the X-23s. Each of those projects could be anywhere in the range of "terminated due to rebellion," again like the X-23s, to "complete failure, recover what you can and try again." It would be weird for them to bother making the 23s and 24 if they did have a Super Prototype lying around.
The "Westchester incident" is described as causing several deaths and hundreds of "injuries". If it was similar to the seizure seen at the beginning of the movie, it would cause two kinds of "injuries" — relatively minor ones from falling over after being caught off balance and permanent brain damage from being unable to breathe for not quite long enough to die from it.
While not confirmed, it is highly likely Kitty was among the X-Men killed by Xavier's seizure. After all, if she survived, Logan would've had every reason to have her send him back in time again.
You're assuming Kitty even developed her time-travel powers in the new timeline in which Logan is set. There's no indication she would have in a timeline where the Sentinels weren't on the verge of wiping out mutantkind.
One depressing thing to realize: since humanity did wipe out mutantkind (albeit with genetically modified corn syrup, rather than overt genocide), this means Magneto was right all along. One can only wonder how that sits with Charles during his lucid moments...
Gabriela mentions that she and several of the nurses were attempting to save as many of the children as they could. By the time Logan and Laura reach the Eden rendezvous, none of the other nurses are there, and Rictor is the one in charge. Considering what happened to Gabriela when Pierce caught up with her, it's highly likely the other women sacrificed their lives to buy the kids time to escape.
You remember that scene in X2 where Stryker used Xavier to mentally attack mutants? This time Xavier unintentionally did it himself thanks to a seizure, and this time the X-Men couldn't stop it.
):In The Wolverine, Yukio, who has the mutant ability to see the death of anyone, becomes alarmed halfway through the movie when she sees Logan's death, describing it as him being "On his back, there's blood everywhere, holding his heart in his hand". In the movie it is played up that he may die when he performs open heart surgery on himself to remove the little robot that is restricting his powers from working properly. But then he doesn't die (Or at least dies for a second and then is resuscitated by his healing factor). Turns out Yukio was wrong.