Time Police: The Da Vinci Codex
A young Leonardo Da Vinci is taken by the Time Police, (A secret time travelling organisation comprised of clones of only the top achievers dedicated to protecting the human race) and cloned. He is taught the ways of the Time Police, and works in the laboratory creating devices for the other officers to use. When they are all killed by a hostile alien race in the year 2445, Da Vinci is humanities last hope for survival.
He goes through a Jean Claude Van Damme style training montage at the beginning, which doubles as the tutorial, and turns him into the greatest ninja ever. You travel to the year 2435, ten years before the invasion when the aliens are still travelling to earth, and using a new hyperdrive engine you built, travel to their mothership and board it. You have to fight through the mothership and destroy it, at which point you escape the blast by using a teleportation device you created earlier on and set with coordinates for the aliens home planet.
The Sequel: Time Police 2 Master of the Arts
Da Vinci is teleported to the alien planet, and finds that it is a giant staging base, constantly creating evil cloned aliens and invasion fleets to wipe out all life on the galaxy. You have to fight through all the alien armies until you get to the control room, in which you find a super A.I. who is orcastrating the whole thing, and enslaved the aliens. He is completely indestructible, so you instead destroy the machine that brainwashes the evil aliens, and they are freed, they turn against the evil computer and manage to destroy it by catapulting the planet into the sun, and then they set off in their many ships to find an empty planet to peacefully live on. You teleport back to the Time Police headquarters to find all the other police still alive.