Fringe Connections

Walter looked at Peter's coin in "Novation" from the night Peter died in "Peter".

Olivia pulled up a list of the frozen heads found in S02E04 'Momentum Deferred' and they were all marked with "2E204", a reference to the episode in which they were stolen.

The butterfly glyph can be seen on a door in the pocket universe.

The bus in "The Ghost Network" was ambered. Huge sections of cities were ambered in the Redverse in "Over There (Part 2)".

The episode opened in "Manhatan", seemingly a typo but actually signifying this was an alternate Manhattan.

A seahorse can be seen on Peter's luggage.

Walter gave the Child M&Ms in the pocket universe in "Through the Looking Glass and What Walter Found There" because he ate them with Olivia in "Inner Child".

William Bell's name is partially faded/scratched off of the door to the lab.

The butterfly glyph can be seen outside the entrance to the daycare center.

Walternate has three solid-color panels on the wall of his office in "Bloodline": blue, red, and yellow. These symbolize the two universes (blue and red) and the rewritten timeline without Peter (yellow) starting from "Neither Here Nor There".

When Walter explains that his red/blue lensed glasses were created by his friend from Washington, Doctor Jacoby, he's referencing the television show 'Twin Peaks' which also had an eccentric man of science, Doctor Jacoby, who wore red/blue lensed glasses very similar to Walter's.

A butterfly can be seen attacking Mark Young.

Cecil mentions the Observers using a light bomb in "Through the Looking Glass and what Walter Found There", which is what Loyalists threw at Peter in the sewer tunnels in "The Bullet that Saved the World".

Who did the Observer say was "still alive," Peter or Walter?

A butterfly can be seen on a lampshade near the front of Olivia's apartment.

The intense amount of Cortexiphan coursing through Olivia in "Brave New World (Part 2)" was able to heal her mortal wound. This was foreshadowed in "Brown Betty" when Olivia was sliced by the same weapon that killed Rachel, yet instead of dying Olivia's skin started to heal itself.

Madison Square Garden in the Redverse is quarantined in amber.

The butterfly glyph can be seen near Lincoln in the rail yard.

September loads his food with heat (pepper, jalapenos, hot sauce) in "The Arrival" because his emotions are dulled, as he explained in "The Boy Must Live".

The Redverse traded Alt Broyles for Fauxlivia by cutting off one of his legs to make their masses equal.

The hand glyph can be seen on a door in the pocket universe.

The End Dock Stabilizer's lights in "An Origin Story" flashed the 'green-green-green-red' pattern from "The Equation" when Peter finished assembling it.

The yellow dot in the final glyph of the episode is replaced by a yellow heart.

Butterflies can be seen on a box in September's apartment.