I'm pretty sure this has been said before but you should add a New Game + feature were the player keeps all their levels, stats, and etc but nobody remembers them, nothing has happened yet, or anything.
Maybe you could make it to were, at the end, when the player can dream to go back to the facility, they decide to stay awake during the travel. This will eventually leading up to a scene/event were, lets just say in a fight, they end up getting a machine, device, or something of the sort used on them, causing them to go back in time or end up in a coma, going through what they did already, allowing them to make new choices or just replay scenes. This option allows you to start at the very beginning, were as the dream option is just to continue were you left off. You should always wake up from the dream to start the New Game + feature.
I know that this is just a shit idea and could mess up the story in some way, but it would be a good way to explore other choices which would have been hard to do since the player was so weak during the start.