As a fan of the X-Men comics, I don't mind admitting that seeing X-Men: Apocalypse was an absolute blast, and it even garnered praise from a Marvel Civil War writer. For me, it was the first X-Men film to truly feel like the comics I grew up with, and the experience was a joy. That said, despite its high box office earnings, it's hardly a perfect film, as fans and critics have pointed out. There are at least two gaping plot holes. So, in the finest tradition of Marvel Comics, here I'm going to look at those plot holes and try to find a way to resolve them!
Plot Hole One: The Prisoners
When Josh Helman's William Stryker enters the film, it's to devastating effect. He arrives at a ruined mansion and uses a sonic bombardment to cripple the mutants. Then, he leaves with the prisoners: Nicholas Hoult's Beast, Jennifer Lawrence's Mystique, Rose Byrne's Moira MacTaggert, and Evan Peters's Quicksilver.
Of course, he's made a mistake. Three mutants — Tye Sheridan's Cyclops, Sophie Turner's Jean Grey, and Kodi Smit-McPhee's Nightcrawler — had separated from the others. With Jean hiding them from the soldiers' view, the three young X-Men are teleported aboard Stryker's helicopter and make the trip to Alkali Lake with the older heroes.
Here's where it all falls apart. When they teleport aboard, they're in the same cell compartment as the others. Stryker then activates some sort of inhibitor field, neutralizing all powers in this part of the helicopter. As a result, Jean can't get into anybody's mind and Nightcrawler can't teleport anybody out. It's an essential detail to explain why the kids don't just teleport the older mutants out but instead have to travel to Alkali Lake.
The next thing we see is that the older mutants are transferred to cells, and the younger superheroes have escaped to wander round the base (Jean using telepathy to prevent soldiers seeing them). Given that they were powerless, how is it the soldiers didn't see the young X-Men when they went to get out their prisoners?
My No-Prize Bid
Here's an explanation. I'm going to presume that part of the cell-system is an electrified cage (analogous to the cage fights earlier in the film). So the soldiers wouldn't be going into that compartment while the cell-system was active. Instead, when they arrive at Alkali Lake, they check whether the restraints are still in place electronically. Seeing that they are, they turn off power to that system in order to take out their prisoners. The younger X-Men, able to use their powers again, get off quickly.
I don't mind admitting that it's a clumsy solution, but it works.
Plot Hole Two: Apocalypse's Goal
Unfortunately, that's not the biggest plot hole. The biggest is undoubtedly Apocalypse himself, whose goal is to destroy a corrupt world-system and create a world where only the strong will survive. He intends to achieve this through Magneto's devastating blitz on the planet.
Unfortunately, this strategy is kind of weird. Michael Fassbender's Magneto simply wants to make the world pay for everything it has cost him, and he lashes out in grief and rage. It's not entirely clear what he's doing tapping into all the metal in the world, unleashing it in a devastating storm across the planet, flipping the Earth's magnetic poles, take your pick. But it's pretty clear Magneto intends no one to survive.
It doesn't matter if you're human or mutant. If you're caught in the metallic storms engulfing cities across the planet, you're dead. Oscar Isaac's Apocalypse wants there to be "strong" survivors, but the only survivors will be people who live in remote areas — regardless of their strength. Why is he having Magneto do this?
My No-Prize Bid
I think that, by this point, Apocalypse has become fascinated by Jean Grey's visions — he glimpses them through Xavier's memories. As a result, he's no longer acting in accordance with his own desires. He believes he's simply fulfilling a prophecy. And he sees the world end in fire.
All of this means that Apocalypse has lost all perspective. He's playing the role he believes that he must, ushering in the end of the world. He's simply assuming that the strong will survive that.
So there you have it! Two major plot holes in X-Men: Apocalypse explained! In the fine tradition of Marvel Comics, I'm making my No-Prize bids!