"One year has passed since the "Third Energy" incident... Dr. Kirk's research on "Third Energy" has been taken over by a government agency, and massive research has begun at a base somewhere in the mid west. However... In the pursuit of immediate results, they have failed to take the necessary precautions, and once again an accident has occurred. This time, the entire research base, military institution, and a small town close by have disappeared. In their place there now lies a jungle from another time..."
— Dino Crisis 2 prologue[notes 1]
One year has passed since Regina's fight against the dinosaurs, and the capture of the rogue Dr. Kirk. Third Energy research continued recklessly at a government-run research base. Suddenly, the research base, military institution, and a nearby small town have completely vanished, mysteriously replaced by prehistoric jungle. Now, a search and rescue attempt to recover survivors and locate the missing Third Energy research data begins. A Tactical Reconnoitering and Acquisition Team is sent into another time frame, which Edward City had disappeared into. Regina, an agent with the Secret Operation Raid Team, has been sent along due to her previous encounters with dinosaurs. On the island, the team sets up camp, but is quickly attacked by an enormous pack of Velociraptors, and everyone is killed except for team leader Dylan Morton, Regina, and David Falk. Dylan and Regina are separated from David (who is fortuitously encountering heavy firepower) and eventually they decide to split up in order to cover more ground.
As the two struggle to stay alive, they encounter leather-clad helmeted inhabitants who are hostile towards them, but their female leader, a girl named Paula is easily captured (saved, really). Though the girl is hostile towards Regina, she acts differently towards Dylan, almost as though she knows something about him. After constantly fleeing from the two heroes, she eventually leads Dylan into a large base complex where she shows him a recording that reveals the truth.
In the future, it is discovered that the 2009 overload in the Borginian Republic had consequently caused time alterations to the Cretaceous Era that would lead to disastrous results. The space-time skew would take its effect on all living organisms and would alter the Earth's history dramatically; preventing the human race from ever existing. To fix this, the international organization WAPP decided to transport all the creatures to a similar environment, 3 million years into the future, where they could thrive. They would then be sent back to their own time (bef.65 million years ago) when the crisis passed. This was called the "Noah's Ark Plan". However, the team suffered another overload when they were about to go back, and their Time Gate was destroyed. Thus, the team was trapped with the dinosaurs. All the survivors were killed, but their children were saved and brought to the safety of the Habitat Support Facility, where they were kept in life support chambers. However, the machines were meant for dinosaurs, and long habitation caused them to loose their ability of speech (although they could regain it) and internalize instinct to protect the dinosaurs. These children are the mysterious helmet-wearing teenagers Regina and Dylan encountered throughout the game. Apparently, one of the members of the team that came to the future was Dylan himself, older. His daughter, Paula, is the blonde haired mystery girl. It appears that in the overloading incident, Edward City itself had been transported to the same future.