That confused me for several minutes, too. I was thankful for the "Year 1" titles and so on. It still wasn't until around Year 20 or so that I'd fully caught on that they were looping back around to what we'd already seen, showing the future for the "first" Joe that ended up with him getting sent back in time without the hood on and saving himself from getting shot, in the present.

Which is actually our future.

Once I caught on, I was happy with the movie for trusting my intelligence enough to let me be confused for a minute. But then came the ending, where I was back to feeling like the people who complained about "aliens" at the end of A.I.