While it's a horrifiying moment, Mystique's mouthing "I love you" to Hank as she's dying is this.
Scott affirms his decision regarding Jean's rampages with a speech towards some of Xavier's students, who assume that Jean is evil by killing Mystique:
"She didnt know what she was doing. Jean lost control. But shes still Jean. Shes still our friend. We can still help her. We can find her. We bring her home. Thats what were going to do, okay?"
When an enraged Phoenix peers inside Charles' head she sees her father on the day he gave her up, proclaiming she's a lost cause - and then Charles' angry rebuttal that as long as there's someone to believe in her that will never be the case. While Charles' actions deserve quite a lot of flak in this film, there's no doubt he really did have the best of intentions for her.
Hank and Erik putting aside their quest for vengeance to protect Jean from the D'Bari. Made even more so by Hank answering Selene's question of what he's doing with "What Raven would!". Selene and Ariki also joining them can allow one to remember one of Logan's lines from the last time the Dark Phoenix Saga was adapted to film.
Logan: Then we stand together, X-Men, all of us.
Charles helping Jean realise that the X-Men (and even Magneto) are her family, and that she should fight for her family. Cue her derailing the train they're on, attempting to kill off many of the D'Bari as possible, while creating force field bubbles around the heroes to protect them from the train crash. And then she curb-stomps the remaining D'Bari into actual dust.
The final scene, with Charles and Erik reuniting one last time to play a game of chess and Erik offering to give him a new life in Genosha. It's heartening that despite everything that's happened between the two over the course of these films, they end the new series as they started it - as friends. And the chess game that ends the X-Men's 20th Century Fox tenure references the two's last scene in X-Men, bringing the series to a sweet, full circle.
Erik: Fancy a game? Charles: No, not today, thank you. Erik:A long time ago, you saved my life, and you offered me a home. Id like to do the same for you. Just one game. For old times sake. [Charles thinks for a moment, before choosing his chess colour from one of Erik's hands.] Erik: I'll go easy on you. Charles: No, you won't.
There's also Erik noting he's checking in on an old friend when he meets Charles despite telling Charles to "stow the old friend shit" before their earlier confrontation, reaffirming their friendship is still strong when he's not letting his emotions rule him over Mystique's death.
In spite of everything that's happened, it's comforting to know that somewhere between 1992 and 2023, Charles and Jean will return to the school and the future for mutants still looks bright.
The "X-Men Legacy" video made to promote the movie is ABSOLUTELY this for fans of the X-Men series who had stuck through it since the first X-Men movie all the way back in 2000.
"Thanks to [Simon Kinberg and Sophie Turner] for bringing Jean's story so wonderfully to life! Essentially true to the original comics story, it turned the focus of the X-film from Charley & Eric (& Hank & Raven) to the students, to Scott (& Ororo & Kurt) & most of all, to Jean and did so brilliantly."