Well in the comics, the phoenix force enters jean when she sacrifices her self for her fellow X-Men... they go all into outer spacy to do some mission (Of which its been so long since I've read it) but on the way back, re-entry into the atmosphere gets a little shakey and Jean sees only one way to save the X-Men and that's to use her powers to shield them from the radiation...
The shuttle crashes into some kind of sea/bay... and the phoenix emerges.... except along the way 'The hellfire clubs' black king tries to harness the phoenix force by trying to control Jean thus making her the Black Queen... that doesn't last long... the Phoenix Force isn't something to be contained... but soon the Phoenix goes a little gaa gaa... feasting on a planet to replenish her energy, thus causing the Shi'ar (Sorry forgot to mention, the Phoenix is the gaurdian of a power kept bye Lilandra the Shi'ar Queeny type) empire to try and contain the phoenix and much to the X-Mens sorrow... The Shi'ar empire wishes to put Jean to death, the X-Men fight for her life but bearing the weight of what the phoenix force has done to those countless millions Jean only sees one option, and that is to say goodbye once again....
That's the general jist from what I can remember... oh and Cyclops finds out his father is one of the 'Starjammers' (Intergalactic Pirates) 😀 I can't see them following the story to a T but still... Phoenix is an amazing story....
Oh yeah and then later on, the Avengers find a cocoon deep in the waters where the shuttle crashed... turns out that the Phoenix wasn't jean at all.... 😀 well it was... had her memories and such but still you know what I mean...
I'm just happy they're taking route... 😀