To say the least...Spoliers ahead.
Tom Cruise's character is Jack Harper, one of the last people on Earth. The planet is abandoned, devastated in an alien invasion. Now everyone lives on Titan, but Jack and his partner Victoria remain behind to maintain the security drones that deal with the surviving remnant of the alien invaders and protect the massive machinery that is collecting all of the world's resources for the people of Titan.
This is all a lie. Jack is actually clone of an astronaut who was the first humans to encounter the Tet, an alien space craft that looks like an inverted pyramid that came to Earth to invade. Basically, he's a Sontaran (an apt comparison considering how short Tom Crusie really is) and his cloned brethren were foot soldiers in the invasion. With the war over, only a handful of Jacks remain, serving as technicians to keep the machines running. Supposedly Jack and Victoria had their memories wiped before the mission as a security precaution, This particular Jack, Technician 49, has been trying to remember his past and has been developing some individuality. Saving mementos of the lost past, and building a house out in the woods as a getaway.
The remnants of the human resistance realize this Jack is different and try to recruit him to help with their plan to destroy the Tet. This plan gets a boost when Julia, the wife of the original Jack Harper returns from space. She was on the mission with Jack and Victoria, but she and the rest of the crew were in cryosleep.
When Jack finally meets another clone, assigned to the next territory and just as unaware of his true nature. He finally decides he will help stop the Tet by flying a nuclear bomb into the heart of the alien ship. He and the old leader of the resistance, played by Morgan Freeman, set the bomb off just a the a fleet of drones is charging the human settlement. The movie ends three years later, Julia has been living alone with their child in the cabin Jack built. The remnants of the resistance find her, and they are accompanied by Jack Harper, Technician 52, who encountered Jack 49 and Julia out in the desert.
Maybe some kind of aliens like the Tet has come to Earth during it's abandonment, and try to claim "squatter's rights" on the world. The Slitheen family has had plans for the Earth in the past, maybe with humanity out of the way they might try something, building massive equipment to extract the raw materials from the Earth to sell across the galaxy.
Going back to the Sontaran angle, maybe someone like Jack could exist? What if a Sontaran ship, with it's crew dead and the bank of genetic material for new clones compromised, came up with a plan to continue it's mission by using another sentient as a source for it's army? That would be a surprise for the players, to see an army dressed in Sontaran uniforms, carrying their weapons, but beneath the helmets were actually humans. If the clones thought they were Sontaran, and not human, and trying to get them to overcome their programming might be quite a challenge.