When you first encounter The Mohole boss fight, Super Joe will normally tell Spencer:


However, there is a chance that Super Joe will instead say something bluer:


The closed captions do not change to accommodate for the dialogue change, making it a surprise. It's not known if there are any pre-requisites to triggering this secret, or if there is just a randomized chance of hearing it, but it can happen if you die to the boss and attempt it again at least once.

In various locations within the game you can see billboards advertising Tricell, a pharmaceutical company from Resident Evil 5.

After the ending credits, there is a morse code conversation between two unknown people. The first massage says "Vault facility occupied. Project Vulture Sentry System has been disabled. Awaiting instructions." The second is a German sentence, that when translated says "Confirmed. Implementation of phase Two. Activate project ALBATROSS." This was meant to set up for a sequel that (at the time of writing this) has yet to be announced.