In X-men: Apocalypse it appears that the Phoenix is just Jean’s power fully unleashed instead of the cosmic being in the comics. However, it should be noted that Mike Dougherty who had a hand in the writing X1, X2, and X-men: Apocalypse had this interesting idea for Jean in X-men: The Last Stand.
“Ultimately she kind of becomes that cosmic force that Phoenix is known to be, she choose to leave Earth and become a god, or at least a higher level of intelligence, and she goes into the cosmos possibly to kick-start life somewhere else… The final scene for me would have been her telling Cyclops or her telling the X-Men ‘I’ll be watching.’ Essentially she becomes a god.“
So the creative team still wants a cosmic being in the films and producers have also said they want to take the X-men into space. There is evidence of a cosmic Phoenix in the film universe. Such as Apocalypse at one point saying “All will be revealed, my child” to the X-men and when he sees Jean’s power unleashed he says in awe “all has been revealed”. And when Xavier looked into his head it seems like Apocalypse had the same visions as Jean did in her dreams. He says to Xavier: “You’ve seen it, haven’t you? The glory of what’s to come?”. All of this seems to imply that Apocalypse has known and waited for the Phoenix for ages.
Singer has also hinted that Apocalypse had powers that didn’t come from earth. There is indeed the question about where Apocalypse’s essence transferring technology that kept him alive in new bodies came from. In the comics Apocalypse had gotten his hands on technology by aliens known as Celestials. With this technology he managed to upgrade himself, giving him several other powers in addition to his own. But its unlikely that Fox has the rights to Celestials and we already saw them in Guardians of Galaxy. So its likely that Fox will do the next best thing and make the aliens the Shi’ar instead, whom they surely have the rights to and there are plans for a faithful adaptation of the Dark Phoenix Saga.
If I had to guess, they are probably mix the Shi’ar empire with elements of the Ultimate Universe’s Church of the Shi’ar. Which was a cult that worshiped a Phoenix God and Jean Grey was the reincarnation of that entity instead of being symbiotic host like in the 616. Basically, Jean had inherit cosmic powers much like in Dougherty’s idea for X3. Thus, that’s how Apocalypse may have learnt of the Phoenix in the film.
Both Marvel Studios and Fox have combined elements of the 616 and Ultimate universe into their movie universes. The biggest example being Mystique’s character. Her Ultimate counterpart has a history with Charles Xavier being his former lover. In the films she is given a relationship with Xavier, but instead she is a non-blood sibling who has been both foe and alley to the X-men. Much like the Juggernaut is in the 616.
The most recent amalgamation between the 616 and Ultimate verse Fox has done is with the character Apocalypse. His background is that of the 616: He’s Egyptian, he body hops, been worshiped as a god, has a Darwinist ideology, alien connections, and four horsemen. But his power set is that of the Ultimate version: amassing other mutant powers, has a healing factor, telekinesis, psychic defense, control over other mutants(somewhat), and super strength.
Just like in the movie Ultimate Apocalypse tried to take Xavier’s powers, gets into a mind battle with him, and then he gets defeated by Jean with the power of the Phoenix. Also just like in the movie, Jean was having visions of the Phoenix which drove her crazy. So the film makers have clearly been reading Ultimate X-men and that’s why I think they will likely go the Ultimate route with the Phoenix. Which I actually prefer over the symbiotic bird because it makes Jean being cosmically powerful on her own is more impressive.
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