Right this is how it goes. You know every know and then you do a mission where you play as John with that army team? Well that is the present. The main missions (where you have the powers and such) they are a possible future. So they aren't actually happening. That's what
could happen if John gets captured.
That's why in the 'possible future' you have all the powers but in the present, John is only just getting them.
It's like a flashback but in the future
.