- Audio Commentary: Director Barry Sonnenfeld. He speaks on the construction of the opening television moment, visual effects work, the performances and greater bodies of work of the cast, shooting locales, the ups and downs of the shoot, and more.
- Alternate Ending (480i, 2:13).
- Blooper Reel (480i, 5:09).
- MIIB: ADR (480i, 9:25): A look at the "Automated Dialogue Replacement" or "looping" process, with interviews, clips form the film, and footage from the looping sessions.
- Design in Motion: The Look of MIB II (480i, 10:01): A look at the involved process of production design.
- Rick Baker: Alien Maker (480i, 10:46): The Alien Designer discusses his work on the film.
- Squish, Splat, Sploosh: The Stellar Sounds of MIB II (480i, 8:04): A look into the process of creating the film's many unique sound effects.
- Cosmic Symphonies: Elfman in Space (480i, 12:52): A glimpse into the world and work of the film's famed composer.
- Barry Sonnenfeld's Intergalactic Guide to Comedy (480i, 6:00): Cast and crew discuss the director's unique Comedy style.
- Creature Featurettes (480i): Short behind-the-scenes looks at the following characters: Frank the Pug (5:03), Scrad/Charlie (2:59), The Worms (3:49), Serleena (4:04), Alien Esoterica (5:26), Jeebs (3:30), Jarra (4:21), and Jeff the Worm (3:35).
- Serleena Animatic Sequence (480i, 1:51): A rough computerized rendering of one of the film's early scenes.
- Multi-Angle Scene Deconstructions (480i, 1:51): Viewers may browse various effects layers by utilizing the "angle" remote control button during playback. Scenes include Opening Sequence: Alternate Version (1:51), Jay and Jeff (0:57), Car Chase (3:14), Jarra Fight Scene -- Part 1 (0:39), and Jarra Fight Scene -- Part 2 (1:00).
- Music Video (480i, 4:39): "Black Suits Comin' (Nod Ya Head)" by Will Smith.