This would leave the second part of the story to be told in X-Men: Dark Phoenix, which would introduce a new, still unspecified, antagonist to be played by Jessica Chastain, and a further-destabilized Jean going full Phoenix during the film.
With Jean already using her Phoenix powers in X-Men: Apocalypse, there’s a chance that the third film in the First Class trilogy just might have been part one.
Then again, looking back at the vague “two parter” set-up that Olivia Munn has mentioned, there’s another possibility at work.
Either scenario could be in play, but we’re betting that due to the fan reaction to X-Men: Apocalypse, this two-parter concept will be starting with the next film.