After cosmog and lillie are captured by Aether, the same stuff happens, with player/hau/gladion infiltrating aether and trying to save them. The difference here is that Lusamine has less an interest in capturing ultra beasts, and an obsession to go through the wormhole and battle necrozma herself to "save" the pokemon of the region, i.e. so she can continue freezing them like a psychopath. However we learn her madness was due to losing her husband to a wormhole, which gives her some motivation in trying to make sure the ultra beast threats don't harm anyone else. She and Guzma leave in the wormhole again, but this time to battle necrozma.
The recon squad fears she will only make it worse, and through legends of the region realize that solgaleo/lunala (an ultra beast in their world) countered necrozma in the past and saved the region from it, so this time the motivation to awaken the legendary is not just to open wormholes and rescue lusamine but also to directly counter necrozma to defend alola. Poni island stuff happens, but there's some differences, like more stuff happening on exeggutor island and Mina having a trial.
You awaken NEbby and cause it to evolve, but when it opens a portal to get to megalopolis, lusamine and necrozma fly out, necrozma having gone on a rampage the moment lusamine tried to stop it. Necrozma's in a rage and looking for light, so it battles Nebby, but you know where this is going and takes it over, using it's light to power itself. It opens portals all over - much like lusamine did in vanilla SM - and retreats to megalopolis. You follow it in, battle it, the thing runs off to be captured later, and Nebby goes to Aether foundation to recover.
Yeah, Lusamine really loved her husband so she went full chosen one and revenge obsessed
