During the siege, one of his mutant horsemen was able to protect him from the debri that was falling on top of them for a short period, until that horseman was eventually crushed by a large stone. This eventually leaves Apocalypse trapped in a pyramid for over 5000 years. 

The next time we see Nur is when he is inadvertently awakened by CIA agent Moira MacTaggert when on a mission to research the ancient cults dedicated to En Sabah Nur, she finds the resting place of Apocalypse (same place as from the ancient Egypt scene), finishing his resurgence process due to sunlight entering the cave through its opening. 

And here is where my theoretical analysis begins:

Apocalypse has said countless times that he has been known as many names, naming a few like Krishna and Yahweh as we saw in the trailer and in the movie when he recruited Storm in Cairo. 

Adding on, Moira has researched many cults that have followed the stories of Apocalypse religiously, as we saw when she presented her Level-5-Clearance report to Professor X and Havoc.

Now, what doesn’t add up is that if Apocalypse has been influencing the outcomes of the world, going as far as presenting himself as a god to many different civilizations throughout history, then how could that be possible if he was found in the same state of being at the same last place we saw him? 

In other words, Apocalypse has been sleeping for exactly 5581 years since 3600 BC waking up in the year 1981 AD, so his mythology enters a paradox. 

In turn, Apocalypse has not been influencing the world since his demise in ancient Egypt. This is true because the conscious transfer was not fully completed due to the lack of sunlight (The golden liquid that flows upwards on Apocalypse’s resting surface seems to be powered by solar radiation). 

When the horseman from the ancient Egypt opening scene is protecting Apocalypse from the falling debris, she creates an illuminated force field around Apocalypse, causing the rubble to contract and entrap Apocalypse in a cave-like structure, forbidding light to come in contact with the mutant. 

This is the same cave-like structure Apocalypse is in when Moira finds him in Egypt. 

Also, Moira MacTaggert’s report only brings her to Egypt, and while it’s possible that the cult could be active somewhere else around the world, keeping to the notion that Apocalypse might never had in fact left Egypt, then Moira is only in Egypt because En Sabah Nur and his cult are only based in Egypt. 

So is Apocalypse a liar? Is Moira MacTaggert and the Intelligence Agency creating false reports?

Let’s say he is actually lying, that still wouldn’t tie in to the story arc since all the names he said he has been called by, except for Ra, are names tied to religions that originated thousands of years after Apocalypse’s fall in Egypt. So he would have had no knowledge of those names. 

When he was in Storm’s home and was “learning” as he said when he was connecting his mind to the frequencies of the television’s waves, that is when he acquired all the knowledge of the past and present world, leading to his ongoing rant about superpowers (USA and the Soviet Union). 

It is after that camera shot that Apocalypse then tells Storm that he is called by many religious names. So, it is possible that Apocalypse is actually lying about everything, fabricating a false history to reinforce his mythology of immense mutant powers, only to con other mutants into joining his false revolution. 

X-Men: Apocalypse | REVIEW

Another supporting premise is when Magneto asks Apocalypse where he was when his parents were taken away by Nazi officers during World War II, and Apocalypse tells him he was sleeping for a very long time. In the comics, Apocalypse is known to enter a dormant stage in his artificial-intelligent craft, Ship, where he sleeps for centuries, later to be waken up by some kind of interference. 

The difference in the movie is that Ship has been replaced by the golden liquid surface we discussed before, and the only reason he was in a sleeping stage was because the initial conscious-transferring process was not finished. 

A counter-argument to that notion is that when Apocalypse was trying to use Professor X as his new host in the new conscious-transfer process, when Nightcrawler teleported the Professor out of the golden liquid surface, Apocalypse woke moments after the disturbance. 

In that case, there was sunlight all throughout the pyramid temple they were in, so right after Charles was physically disconnected from the ancient golden machine (they still held a mental connection afterwards), Apocalypse was able to quickly awake because it was still being powered by the ongoing present sunlight.

So, in the movie Apocalypse has only been king of Egypt, and of any other civilization that came before, giving to the possibility that he lied to his henchmen about his history, or Moira MacTaggert had it all wrong, or maybe this was something Fox totally missed, but there is probably, hopefully, a valid explanation.

You can watch X-Men: Apocalypse now in theaters. It stars Jennifer Lawrence reprising her role as Mystique, James McAvoy reprising his role as Professor Xavier, Michael Fassbender reprising his role as Magneto, Nicholas Hoult reprising his role as Hank McCoy/Beast, Oscar Isaac as En Sabah Nur/Apocalypse, Game of Throne’s Sophie Turner as Jean Grey, Tye Sheridan as Scott Summers/Cyclops, and Olivia Munn as Elizabeth Braddock/Psylocke.