Dark Phoenix: The Dark Phoenix appeared often during the flip through comic Marvel uses at the beginning of each movie. Is it coincidence that the next X-Men film is centered around the Dark Phoenix saga? Maybe, but it makes sense.
Alkali Lake: There is a lot of history at Alkali Lake in the X-Men Franchise, as this is where Colonel William Stryker turned the “Wolveringe” into Weapon X. Donald Pierce and his “Reavers” have ties to the same company that created Wolverine.
Greenwood Cemetary: In the movie, Logan is seen as a limo driver chauffeuring people to this place. This specific cemetary has popped up before in the comics, and though no specific characters were laid to rest here, it has appeared in titles such as 'Fantastic Four' and 'Deadpool: Too Soon?.’ There is also a grave that reads “Peters” behind Logan. This could be a tribute to Evan Peters, who instantly became a fan favorite for his role of Quicksilver.
Wolverine vs. Freddy Kruger: When Donald Pierce first meets Logan’s character in the back of a limo, he compares the Wolverine to a tiger or Freddy Krueger. Fan fiction pits these two together quite often.
MMA fighter Krzysztof Soszynski: You might have missed him, but he will be remembered as the man who lost his head during the first fight scene featuring X-23.
Cage Fighting: Early in the movie Logan and Xavier reminisce about how they first met in the original X-Men movie. Xavier described how he found Logan Cage fighting, before stating, “We took you in and gave you a family."
Statue of liberty: In another reference to the first X-Men, Laura and Gabriela Lopez are hiding at the Liberty Motor Motel. When Xavier tries to tell Logan where they are, the two make reference to the climax of X-Men where the team battle at the real Statue of Liberty.
The Tank: One of the more obvious Easter Eggs is the tank that Caliban and Logan put Professor X in to keep his powers in check. The tank looks similar to the Cerebro room back at the X-Mansion. One scene in the tank also features Xavier rambling on in a hilarious product placement for Taco Bell.
The Reason for the Tank? While Xavier, Logan and X-23 are fleeing, there is a news report on the radio that relates what was happening in the film to an attack that happened in Westchester (where the X-Men Mansion is), which resulted in deaths of some of the team. In the Old Man Logan comics, however, it was Logan that was tricked into killing his fellow X-Men by Mysterio.
Caliban Reunion: In one scene,
Donald Pierce hints that Caliban's mutant tracking abilities were once used to hunt down the last few mutants. Caliban’s story in Logan mimics his story in the comics where he was transformed by Apocalypse into the Horseman of Death.
Bathroom? After Charles and Logan’s scuffle in the rest room, Logan finds a few comic books that reminds him of his past with the X-Men. On his way out from the rest stop he steals a few cigars for the road, which are a big part of Wolverine in the comics.
Comics: The comics Logan picks up in the film are Uncanny X-Men #117 and #132. In Uncanny X-men #117, Xavier tells his tale of how he first dedicated his life to the mutant/human relations, and on the cover of #132 is an epic battle between the Wolverine and Donald Pierce.
Mobile Phone Video: In the video that the nurse, Gabriel took, there are a number of Alkali Transigen case files that flash on the screen. One of the files revealed that DNA was taken (probably stolen) from Christopher Bradley, a mutant who had electrical powers. Christopher Bradley also made an appearance in X-Men Origins: Wolverine as part of Team X.
Mobile Phone Video PART 2! The mobile video also contained footage of Laura cutting her arms just to show off her amazing healing ability. This was a moment that also took place in her origin story in the comics.
X-Force Mutants? In the film, Laura isn’t the only test subject that was used in Rice’s experiments. There are a few other children that are named. First there is Bobby, who possesses the DNA of Iceman or Sunspot. Second is Rictor, who possess the power to create earthquakes. During the final battle another mutant named Joey is revealed. It is very possible that this character could be Jean Grey’s telekinetic nephew Joey Bailey.
The Casino Hotel: During a brief period where the group relaxes, Charles and Laura are watching an old western called Shane. The story of Shane mirrors the film Logan. In Shane, and old gunfighter has one last hurrah in his old age. The words Shane says to a little boy resonate with Laura, who quotes the words for Logan during the films finals scene.
"A man has to be what he is, Joey. Can't break the mould. I tried it and it didn't work for me... Joey, there's no living with... with a killing. There's no going back from one. Right or wrong, it's a brand. A brand sticks. There's no going back. Now you run on home to your mother, and tell her... tell her everything's all right. And there aren't any more guns in the valley."