Well during this current battle he's going to evolve into a Fraxure, then much later on he's going to evolve into a Haxorous, all the while when he's working for Deoxys he'll be recruiting various pokemon he believes can help fight against Deoxys, then, most likely during a major battle, he's going to challenge Deoxys to a battle himself, he'll probably lose but he'll be expecting that, he'll use himself as a distraction while his recruited turn against the other infected during the war, then Sho will stand back up and fight Deoxys again, he might also die in this battle but at this point he doesn't really care as Deoxys army will be defeated/ severely weakened, which will ultimately lead to Deoxys' defeat, once Deoxys is dead, his control over pokemon will be released and all will be well.
Or at least thats the perfect scenario I have in my head and is more what I "hope" to happen, the only things I know for certain is that Sho will eventually become a Haxorous and challenge Deoxys, other than that anything could happen XD