You can activate a secret ending by following the process outlined below.
Make your way to a series of small islands, located east from the mainland.
Once you arrive at the islands, check rock outcroppings. You're looking for a supply crate, which is really just a reference point. When you find it, dive underwater and you should find a less obvious crate resting on the sea floor. It contains a Nuclear Codes item that you should take.
Look for an area with two open warehouses, in the middle of a facility with grain silos. Nearby, you'll see an intersection of train tracks, and the Behemoth monster. In a warehouse, you can grab the Military Transport Key. It's in a container positioned against one of the walls.
Find the lake that has formed near an enormous dam. A body is floating near its center. Check the corpse to find and obtain the Military Activation Key.
Along the eastern side of the map, look for a two-lane road that runs from north to south, a short distance northwest from a town built along the shore. Head along that road and you'll find a military caravan.
Enter the convoy, which requires the items you have gathered: the Military Transport Key opens the entry door (use it on the card reader). The Military Activation Key gives you access to the computer. And the codes can finally be used on the bomb.
Now sit back and watch the ending.