Carefully based in its own mytharc, Fringe revisits the story of Nina Sharp, as re-written by Dr. William Bell and colleage Walter Bishop during their Cortexiphan trials after they failed to save a child circa 1985.
Olivia and Walter investigate the electromagnetic presence haunting them, Dr. Bishop's theory is that this somehow relates to the collateral due to the trials themselves. Since these children's powers were never activated, for Peter wasn't there to help track down the subjects, the only collateral damage of the trials seems to be that Nina Sharp became a foster mother for one Olivia Dunham.
And so, the episode delves in the relationships destroyed and reshaped by Peter's absence. At the same time the audience figures out how each of them fit in each other's lives, the characters figure out the real nature of "Subject 9", a mysterious form who materializes in same frozen lake he was last seen by the people who met him: Peter.