The Future Trunks Arc hasn't been aired yet, the story hasn't been told, how do we know the plot?
But since I have a pretty reasonable answer to share, I might just answer it anyways. But it also contains spoilers, so... yeah.
Based on what I know about the next arc, it's all about time travel, and yes, the game Dragon Ball Xenoverse is all about time travel too, and also the game's sequel, it both featured Future Trunks. If you played the game before, or know a bit about the game. Future Trunks from Xenoverse and Online works for Supreme Kai of Time as her assistant and the head of the Time Patrol, his job is to mainly fixing distorted timelines.
Towa and Mira were the two major villains that travel through time to destroy the history. Besides that, Towa can cast dark magic on enemies which gives the user pure red eyes and a dark aura, pretty much turning them into demons.
So, the evil / black Goku is probably from an alternate timeline (defeated the heart virus) and been cast by Towa's dark magic, and turn him into her pawn to assist her evil plan. Future Trunks from that timeline fought the evil Goku and was overwhelmed, he barely escaped into the main timeline to ask for help once again.
Though, it's just a theory, I might be wrong, or not even close.