Alternate versions

There was an alternate ending that was featured on the DVD. After Captain Michaels announces that they are heading to the Cape of Good Hope, he tells Dr. Helmsley that he has a phone call waiting for him. Dr. Helmsley discovers that his dad Harry is still alive. Harry tells his son that he, Tony (whose arm is in a sling) and some of the passengers and crew survived the mega-tsunami that struck the Genesis. Captain Michaels states that they should have a visual on the ocean-liner shortly. After Kate thanks Laura for taking care of Lily, Laura tells Jackson that she liked his book. Lily then announces that she sees an island. The Arks arrive at the shipwrecked Genesis and the survivors on the beach.

There were some deleted scenes that were featured on the DVD:

• Jackson drives Alec and Oleg to the airport while trying to get through some doomsdayers.
• President Wilson and his secretary Sally talk about plans to make arrangements to address the nation one last time.
• After the discovery that the impact drill is stuck and before the mega-tsunami hits, Anheuser blames Adrian for what his decision cost them and makes a comment about having sex with Laura. Dr. Helmsley punches him before taking Laura and some crew members down to the Hydraulics Chamber.
• Jackson finds Gordon's cell phone under the water after Gordon was crushed by the gears.
• In a follow-up to the alternate ending, Anheuser (after hearing that Dr. Helmsley's dad is still alive) apologizes to Dr. Helmsley for what he said.