The specifics of the story are less important than what they do to Olivia. The invisible man - struggling to become visible, literally dying to do that - became that way due to a genetic condition, treated by a predecessor of Massive Dynamic, with Bell and Nina in residence. This has two effects:
1. Olivia gets more in touch with the treatment Walter and Bell subjected her to.
2. Even more importantly, this gets Olivia to go see Nina. Which sets up the ending: Olivia is knocked out (white gas under her door), and injected with something that will remove her memories from the two hours. In some sense, Nina is now a villain.
But to what purpose? What did Olivia see, think, do, feel in the previous two hours that Nina, for whomever or whatever she may be working for, wants Olive (as Nina calls Olivia in their meeting) to forget? We'll have to wait until January to find out more, but I'm thinking Nina may be working in concert with Walternate.
We haven't seen too much of the alternate universe in Fringe this Fall, but the coming attractions show it will be back in the action.
Both ours and the alternate universe have been changed by Peter's absence, and it's important to bear in mind in which ways the alternate universe has been changed and unchanged from what we knew of it last season (we've seen this season how much our universe has been changed by Peter's absence). Since Peter "died" in the crossing on the iced-over lake, Walternate may hate our universe and Walter even more than in the reality in which Peter at least lived on our side. From Walternate's point of view in this double-universe without Peter, Walter not only kidnapped Peter but killed him.
The resolution has to come down to Peter, now, who is the only witness (other than the Eternal Bald Obersvers) to what we the audience saw the first three seasons. He gives Lincoln a new pair of glasses - to make him more attractive to Olivia? - but the metaphoric implications of this are huge. What's going on in Fringe is how to improve everyone's vision, so they see the truth. Somehow, that reality - ours and Peter's (who is also an invisible man) - has to become visible.
... Fringe 4.2: Better and Worse Selves ... Fringe 4.3: Sanity and Son ... Fringe 4.4: Peter's Back, Ectoplasm, and McLuhan ... Fringe 4.5: Double Return ... Fringe 4.6: Time Slips