Quarantine 2 takes place on a plane. This plane is on its way to Nashville, Tennessee from Los Angeles, California. Ralph is one of the passengers on the plane. He has been bitten by a lab rat which he thinks is a hamster. Ralph becomes violent for apparently no reason which forces the plane to change its destination from Nashville to Las Vegas, Nevada. Having been restrained due to his violence, the plane safely in Las Vegas. The pilot, Captain Forrest is told by the crew that is manning air traffic control to remain where it sits. Captain Forrest disregards the warning and goes to the gate. He allows everyone to leave and attempts to lock Ralph in the plane's bathroom. The co-pilot remains with the captain to assist him.
The passengers, having fled into the terminal are shocked to learn that they are locked into the terminal and cannot leave. The CDC has arrived to contain the situation from getting any worse. They allow a group of people to retrieve a medical bag that was stashed inside the cargo hold. They soon are infected as well since Ralph has successfully escaped from the bathroom.
The group from the CDC goes to inspect the plane and allows everyone from the plane to go into the terminal. They begin curing everyone from the disease. They are not quick enough in curing the disease and soon an infected cat infects everyone in the terminal. The group from the plane manages to escape with one from the CDC's group who reveals that they are from Homeland Security. They are curing everyone from a biological agent that a terrorist organization had created in a lab in Los Angeles. The agent then tells them that the drugs that they are administering is an experimental antidote.