After all scientist have been consumed there is a secret cutscene unlocked that shows Alex finding Karen Parker, Alex’s former romantic interest, who betrayed him earlier in the game. It seems that the intention was that once Scully (the first boss) had been beaten, the kids would start to. As noted in the prototype screenshots, there were originally going to be kids on the bus in stage 1. One of the things a player can do after beating the game is continue consuming targets to unlock new web of intrigue cutscenes that go into more detail explaining the story. One sprite for each character is used in the opening cutscene for stage 5, but the rest go unused. My name is Alex Mercer and my work is almost done.” After the extra scene ‘Free Roam’ mode is activated allowing the the player to continue working towards getting rid of the infection in the city and building up their character’s skills by doing side missions. The Tyranids (WH40k) decide to attack an hiveworld but as soon as the Hive Fleet appears a ROB destroys the Tyranid invasion force leaving only a single Dominatrix alive and a few spores which lands on a random spot on the planet, on the otherside of the planet through some warpmagic Elizabeth. There is a scene showing Alex Mercer standing on top of a building and saying, “One virus.
There are also black and red images of New York in ruins and characters from the game shown alongside the credits. Audio clips of citizens, military officials and the senator of New York discussing the events that took place during the game can be heard during the credits of Prototype.