The first time I read this 3-part extension (or, moreover, gap-filler) of the Fringe story, I was lost as to its meaning. My clearly befuddled review over at Thor's Comic Column [link: http://www.chud.com/70575/thors-comic-column-1014/?textutm_source=chud&utm_medium=&utm_content=&utm_campaign=non_home_clicktracking] is proof of that. The main problem the story had, at the time, was that it came out just as season 4 was starting. Peter had blinked from existence and was haunting the people he loved who had forgotten him, and the big mystery was "what happened to him". I thought this arc, written by series star Joshua Jackson, was a convoluted way of telling us fans of the show that he was lost in time (ala Captain America and Bruce Wayne in the preceding years) but what I wasn't getting was how tightly connected Jackson's script was to the Season 3 finale and less so with the season 4 premier.
My wife (!) and I are steadily trolling through Fringe this year and we just finished Season 3, watching the final episode which both my wife (!) and I had kind of forgotten most of the details of... Peter enters the machine and is thrust into the future (2026) where he'd chosen Earth 1 thus destroying Earth 2. But in reality Walter had drawn Peter's 2011 consciousness forward in time in hopes to influence his decision making in the past. But in order to do so Peter has to close the loop, sending the machine back in time, and Peter with it to bury the machine parts at predetermined markers (where the markers came from and how exactly Peter bounces through time I don't know).
Like hitting up the show proper for a second time there is much illumination in the intricacy department, the gaps its filling becoming far more evident. It's a great little companion story that perfectly bridges Seasons 3 & 4 without spoiling anything or dropping the ball in the details department.