When the Joker announced that he would rule Gotham City at midnight, the police began a massive evacuation of the city. However, the Joker implied that the tunnels and bridges were rigged with explosives, forcing the police to evacuate using ferries. The last ones to be loaded before midnight were the Liberty, which was carrying civilians, and the Spirit, which was carrying criminals.
At 11:30, both ferries' engines stopped and both crews discovered massive amounts of ammonium nitrate in the engine room, rigged to blow. The Joker announced that if anyone attempted to get off, he would destroy both boats and that at midnight he would destroy both. Both boats were given a detonator to destroy the other one. If one boat chose to destroy the other one, he would let the surviving boat go. The civilians on the Liberty debated on whether or not to destroy the Spirit, some citing that the criminals had their chance and should die. Although the majority voted in favor of blowing up the Spirit, no one was actually willing to do the deed.
It can be assumed that after Batman subdued the Joker, everyone on the Liberty and Spirit were rescued.