- There exists an alternate death scene of Serleena that seemingly was filmed but was never released on any home media, outside of an official Men In Black 2 picture book adaptation. The scene in question had Serleena giving Scrad a 'proton detonator' to destroy the MIB Headquarters, only for him to later show up and use it to destroy the Serleena, who had merged with Jeff The Worm.
- Scenes shown in TV spots included two extra scenes in the deneuralizer room (one of K and J at the door and another with K in the chair, both with Jones in the mailman's uniform), and a version of the clothes change montage featuring K's mailman uniform.
- The DVD features an alternate ending which is similar to the ending given in the theatrical release, but with a different location in MIB headquarters.
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