Set-Up: As a child, Anakin Skywalker was speculated to be The One to bring balance to the Force, but, ultimately, let power and hate corrupt him. As Lord Vader, Skywalker terrorized the galaxy, eliminating every other Jedi in the process. He's the commanding officer of the entire Imperial fleet, and lets no mistake go unpunished.
Agent Smith was just another computer program created to eliminate anyone who would dare destroy the Matrix -- the computer generated dream world. However, much like Skywalker, Smith let power corrupt absolutely, broke free from the Matrix, and became Hell-bent on destroying everyone -- as well as the Matrix.
Fearing that Skywalker is The One (who is prophesied to bring humanity back to the top of the food chain and destroy the Matrix) Smith attacks Vader while he rests in his chamber.
Place: Executor, Darth Vader's Super Star Destroyer
Notes: Assume that even the Star Wars Universe is set within the Matrix, and that Neo (and his friends) have yet to be born/created.
Vader has full use of the Force, and his lightsaber. Smith can manipulate the physics of the world/Matrix (as he could in the first film), and has his guns.