THIS ALL DAY EVERY DAY. Seriously. In my mind so much would have been different had Rachel been allowed to be a player in the event. But her relationship to the Phoenix "complicated" their "story".
For me, some of this would have played out similarly, more X-Men would have been injured in the course of the event, leading to a recruitment of of teams, namely Excalibur to come in and assist with the rescue effort. With Scott and Jean in peril, Rachel joins the fray also having strange images of battles and conversations during the series from Cable's perspective (her remnant psilink to him). She and Kitty accompany Cable, Havok, Polaris, and Cannonball to the moon and she is able to also enter the field. Stryfe's power levels are even stronger and he goes ballistic when he see's Rachel appear. "You!! How are you so young?!? This is YOUR FAULT!!" He lashes out at her, leaving him open to an assault from Cable. Similar ending but Rachel realizes that Cable is Nathan at the last moment. She then uses her powers to enter the timestream in search of him, which leads to a small mini and him returning and cements their bond as brother and sister, and helps further connect Rachel to Scott and Jean, as the return of his son prompts Jean to propose and make their family real.
Second Coming:
Plays out similar to everything leading to the creation of the dome. As the war with the Nimrod's rages inside the dome, after Cable and crew have left for DoFP, the X-Men are being beat while their "friends" the Avengers sit and watch. Suddenly a huge light appears over the dome and light punches through the top. It's the X-Jammers with a small Shi'ar army in tow. the portal closes again as the strain of keeping the hole open overloads the Shi'ar tech. Things aren't going well in DoFP, which requires Rachel to use her echo (she still has it) to enter the timestream and see how corrupted it has become after she saved it (Excalibur 68). Cable and Rachel together hold open the timeportal and during this the echo rushes from rachel into the portal, and at the last moment Nate pushes her through to save her. Rachel feels the echo is close and realizes that Hope may be the next host. She then introduces herself as her aunt, and offers to train her.