Infinite seems like he might be dead at the end but it’s not confirmed. Also, Sonic is presumed dead when he is actually alive, which goes on for six months.
Yes, technically. Sonic is a teenager and he gets kidnapped, restrained, and tortured. We don’t see much of it but…yeah. With that said, we all already know Eggman is not a nice guy, we don’t see the torture, and Sonic is rescued and he’s mostly fine when you bust him out of there.
Nameless soldiers are vaporized by Infinite near the beginning of the game. Infinite himself seemingly disappears near the end, but his date is unconfirmed.