The opening credits background are yellow/amber-ish for this alternate timeline created by Peter's disappearance.
The glyphs for this episode spell out: APPEAR
As the two Olivias finish their conversation toward the beginning, if you watch closely, you can quickly see Peter's image flicker in the background as Earth 1 Olivia turns away from the table.
Towards the end of the episode when Olivia is taking Agent Lee to Liberty Island and he scans his hand for admission, a leaf appears on the screen upon which he scanned his hand. The leaf is identical to the leaf shown during breaks used as a secret code for hidden messages.
This season takes place in an alternate time line. Agent Astrid Farnsworth's hairstyle is very similar to how it looked in Season 1.