WARNING: The following article contains spoilers for Days Gone.
After roughly 40 hours of gameplay to complete the main story, many gamers will set their controllers aside and leave Days Gone for good. Other will start up a whole new save file. However, those who continue playing after the credits roll will be rewarded with a secret ending, one that has huge ramifications.
Once the final mission is over and Wizard Island is destroyed, the game's open-world map is still available to roam. From there, players can finish any remaining side-objectives, such as Freaker Hordes or NERO research sites. After a while, the player will receive a radio message from NERO researcher James O'Brian, who will ask the player to meet him.
When protagonist Deacon St. John meets O'Brian at the old cemetery, things get bonkers. In the prologue, the player meets O'Brian, who is wearing a full body hazmat suit and a helmet with a transparent screen. Here, his face is visible. However, throughout the rest of the game, O’Brian's mask is tinted, meaning Deek can't see his face.
The reason for this is only revealed in the secret ending's cutscene: O'Brian is infected. He finally takes off his mask to reveal a ghoulish, vascular visage, causing Deacon to recoil. O'Brian explains that the virus which created the Freakers is rapidly evolving, and it's now at a stage where it can invade the lymphatic system (which helps protect the body from disease and infection) of uninfected people. He also reveals that the higher-ups at NERO have known about this for a while, and warns Deacon that they are coming. O'Brian leaves, jumping into an airborne helicopter with inhuman strength and agility.
This cutscene conveys that this new strain of the virus creates an altogether new form of Freaker, one that maintains the cognitive functions of a human but possesses the strength, speed and aggression of the creatures Deacon fights off throughout Days Gone. In fact, at several points in this scene, O'Brian's body makes seemingly involuntary jerks, and he even takes several steps toward Deek before apologizing. Though it's never explicitly stated, it appears the O'Brian is resisting the biological urge to attack brought about by the virus.
Clearly, this scene was intended to leave the door open for a Days Gone sequel, something that now looks like it will never happen. Instead of the optimistic ending of Deek riding off into the sunset with Sarah, this twist finished the game on a darker, more threatening note. The new form of Freaker introduced through O'Brian would have made for a formidable enemy in a second game, which would surely have followed Deacon's efforts to uncover the truth about NERO's link to the virus.
It's worth noting that, although NERO features prominently in Days Gone, Deacon never actually fights against them. In the missions they're featured in, Deek can only sneak around the soldiers and researchers, as the game makes it clear their suits are too fortified for him to cut or shoot through. A sequel likely would have made NERO the main antagonist, with Deacon and company having to face them head-on. However, as things stand, this is a story that will remain untold.