So, what will the plot of Metroid Prime 4 be?
Tanabe has alluded to a rivalry between Samus and Sylux...and going off of the ending of Federation Force, Sylux most likely will have some sort of plan to use the baby Metroid against the Galactic Federation in some way...
There's potential for some serious stuff going on in the next game...Perhaps cloning to make an army of metroids and literally wage war against the Galactic Federation, perhaps the bulk of the game's story is Samus trying to hunt down Sylux to prevent such a thing from happening...I can imagine Samus investigating abandoned space vessels or GFed outposts or something where Sylux had used Metroids to attack the Federation...similar to the GFS Valhalla or even the GFS Tyr in Echoes...
I've heard some speak about the possibility of Sylux using the Metroid to resurrect or recreate Metroid Prime...I'm not entirely sure how it could do that since Metroid Prime was a product of Phazon mutation and Phazon has been wiped out...
I've also had this idea that Sylux may take command of the Space Pirates, after Prime 3 with the "death" of Ridley and Dark Samus the Space Pirates were left without higher authority (later on the Fed Force defeated Master Brain as well) and since both Sylux and the Space Pirates have beef with the Federation, I wouldn't rule that out as a possibility...