When June came out to the pilot on-line JJ Abrams and the other producers were quick to stress the fact that the incident was not fully completed. In the version we say "Final Cut" there were some new scenes and the soundtrack was entirely new.
In this post we will see what were the changes between two versions of the first episode. Translated from the site
FRINGETELEVISION.COM
FRINGETELEVISION.COM
The opening sequence has been completely renovated. (This I think is very nice) 
Four significant changes have been added in the story:
- Olivia cries when he sees for the first time the agent Scott infected by the explosion, the scene reinforces the feelings for him
- The entire interrogation scene of Steig with Olivia Dunham and Peter Bishop has been completely turned over
- Most audio recorder of Steig's was changed
- The final scene has been enriched with the transport agent in a room where Scott will be questioned when the door of this room opens the symbol of the leaf.
The image above appears at the end of the episode and introduces the brand new trailer for the season. This is a kind of summary on where to look for clues in the episode.
Not only is the company name was changed from a MASSIVE MASSIVE DYNAMIC DYNAMICS, even the building is another that seems to be a typical New York skyscraper.
There are also many changes the scene of the "dream". The picture is much darker, the writing on the headstone and Kayak are different from Preair to synchronize and monitor the minds of the two agents send different images.
Finally, the mechanical arm has implanted Nina Sharp is different from its predecessor. This is transparent and seems to remember much of the agent Scott when the body is infected by the virus
Not only is the company name was changed from a MASSIVE MASSIVE DYNAMIC DYNAMICS, even the building is another that seems to be a typical New York skyscraper. 
There are also many changes the scene of the "dream". The picture is much darker, the writing on the headstone and Kayak are different from Preair to synchronize and monitor the minds of the two agents send different images. 
Finally, the mechanical arm has implanted Nina Sharp is different from its predecessor. This is transparent and seems to remember much of the agent Scott when the body is infected by the virus For an analysis of the pilot episode of Fringe go here:
ANALYSIS COMPLETE FRINGE 1x01 - S01E01 PILOT
ANALYSIS COMPLETE FRINGE 1x01 - S01E01 PILOT
