Olivia's trip to the Alternate Reality seemed to be cut and dry at the end of the Season 1 finale "There's More That One Of Everything". However, as Joshua Jackson explains in this video, that "what you think you saw at the end of season 1, is not at all what actually happened."
Here is a time line of events of what we think happened (our reality on the left, alternate reality on the right):
The shape shifter waits for Olivia to pass by, so he could crash into her.
In "There's More Than One Of Everything", we see Olivia swerve to avoid the accident.
However, if you listen to the audio, you can clearly hear that accident did take place, and Olivia has crossed over into an alternate reality but does not realize it.
Olivia continues in the alternate reality to her meeting with William Bell at the Mutsumi Hotel. When Bell is no show, Olivia enters the elevator to leave the hotel.
Originally we thought this is where she crossed over to the alternate universe, but if she is already there, maybe she is teleporting to the World Trade Center. A similar blue light was seen when David Robert Jones escaped from Wissenschaft Prison.
Olivia meets with William Bell. The rest of the conversation will be coming soon.
Olivia violently returns to our reality.
I think the elevator ride is where things get a little confusing. What do you think happened to Olivia?
If you are searching for a friendly place to discuss the Fox TV show Fringe, or just a resource for keeping up with the latest news, clues and views on the series, you have come to the right place.