Emily, Vigo and Trellis will go and fight Ikol, while Navin, Aly, and everyone else who's not a stonekeeper goes on the colossus (because it's about time we get a proper robot fight) and fight the shadows which have begun to completely overtake Alledia.
My guess is that Vigo is probably gonna die, and Emily will get mad and really use a whole lot of her powers to defeat Ikol. Ikol will then move on to his backup plan, which was to take over Emily's body to destroy Trellis, then completely overtake Emily's body and live inside of her (or may go the other way around, taking over TRELLIS' body and destroy Emily). But the plan fails and Ikol is eventually locked into the Void with no possible way of escape.
Meanwhile, Navin and Aly are completely overrun by shadows, but are saved by Emily and Trellis. Emily and Trellis overpower the shadows and throw them into the Void as well, keeping them in the Void where they won't harm anyone else. Alledia celebrates and Trellis and Riva plan to rebuild the Elf Kingdom. Emily rejoice with Navin and Mom, and even though Emily wants to go back to Earth, she decides that she would much rather stay here to protect people from other dangers.
Jump forward to a few years, and Emily is the most powerful stonekeeper imaginable and adopted a boy named Moze. Emily and Trellis (look, usually I don't ship characters because I think it's kinda weird, even if they're fictional, but I'll make an exception this one time) settle down on the planet Ghen-7 and get married there. They live there for some time before Trellis decided to go back to the nation of the Elves, which has been far more healthier and peaceful than before to take the spot as king. Emily decides to train Moze to be a stonekeeper from another Mother Stone Navin and the robots found while mining in colossus suits. Navin and Aly also marry (this is a ship I think works). The story ends with Emily at the edge of a cliff staring at a sunset or something with the ghosts of Silas, Emily's dad, and Vigo by her side.
This is most likely how it will not end, but I like to make things up.