Adam drops the virus and it gets in to the ventilation system. Parkman, Peter and Nathan find many Primatech workers dead or dying. They go to the police station (a set they reused in the aired version) where Parkman "convinces" everyone to listen to Nathan who wants to quarantine the town. In storyboards Peter creates a landslide to destroy the bridge out of town (the one where the Haitian shot Noah). Kring and co explain that Odessa would be completely quarantined. Nathan gives a speech on TV, watched by Mohinder, Maya and co in New York and Claire in California but collapses having been infected. Claire, Mohinder and Maya would have gone to Odessa - Claire because she thinks her blood can cure Nathan and because she saw that Peter was alive as he was standing next to his brother and Mohinder because he is the world's leading expert on the virus. Maya goes with him because they would eventually become a couple. Mark Harelik's character who Peter met in the future would reappear too.
Eventually, and they hadn't completely made their minds up about this, Maya would prove to be the cure. Her abilities would allow her to draw any sickness in to herself, not just the one she creates. They hadn't decided whether or not this would have killed her.
They also mentioned a scene where some of the people in the town try to leave, forcing the National Guard to gun them down.
Some of this we actually see, while some is just described by Kring as they hadn't shot any of it. The effects are clearly unfinished in a lot of places or are replaced by storyboards and production designs.