The Seed [2006] by Joe Hahn

The Seed follows the events surrounding a homeless veteran named Ken Mercado, played by Will Yun Lee. Living along the banks of the Los Angeles River, he is attacked by masked men in black vehicles, invisible to the eye. To any passers-by, Mercado appears to have some sort of mental illness, but as he is chased throughout the city, it is revealed to the audience that he is not in fact paranoid, but rather the victim of a government conspiracy. Sung's adversaries are visible to him, yet only visible to the audience part of the time. At the end of the film, an alien ship is visible in the sky, watching the scene.