One Observer can be seen walking behind the two men who are talking about getting an approval for level six eradication.
The glyphs for this episode spell out: WINDOW
Like many episodes of Fringe (2008), this one contains several affectionate references to The X-Files (1993): the plot concerns a virus in a black oil that takes over the personality of and eventually kills its host human, something that was also a long-term plotline on "The X-Files"; FBI partners Peter and Olivia have a fight in which Peter (under the influence of the oil) accuses Olivia of betrayal, something that often happened between "X-Files" FBI partners Mulder and Scully while one or the other of them was being mentally altered against their wills; the guest star who plays Steve, Brendan Beiser, was an "X-Files" regular as Agent Pendrell, and Megan Leitch, who also guest stars in the episode played Samantha Mulder.
When the CDC computer shows the simulated animation of the virus spreading, all countries end up being contaminated except Madagascar (shown in black versus red). This is a clear reference to the "Pandemic 2" online Flash game, in which Madagascar is supposedly notoriously difficult to contaminate due to very careful public health policy (airports, shipyards and borders are closed as soon as contamination is rendered public, and so on). In typical games, Madagascar often ends up being the only country not contaminated. However, during the COVID-19 pandemic that started in 2019, Madagascar's fictional epidemiological impermeability was not reflected in real life; as of mid-January 2022, over 55,000 people in Madagascar had been infected and they had experienced over 1,000 COVID-19 deaths.
Walter implies that a rock layer ten miles down is rock from 75,000 years ago. The Grand Canyon is just over one mile deep and exposes rock layers spanning over two billion years.