3. The Pattern
One of the biggest mysteries of Fringe still stems back to the first season (and before). Quite often they would refer to The Pattern, seemingly relating all Fringe events to one another. Broyles, Nina Sharp and other unnamed people were part of an organisation that tracked these events before Olivia got involved, and details of this original setup have been sparse. There were also the hand implants, data discs found in the hands of various sympathisers (including Olivias partner John Scott). Neither of these was particularly explained except for saying Massive Dynamic were investigating it all. The second series jumped straight into crossing Universes, so the story with the Pattern seemed to fade away quite quickly.
The Questions: What was the Pattern, and what were the implants? Did they get dropped to take a different narrative direction? Do they still matter since were in a new timeline? They had already associated the Observers with the pattern, did they cause it?