Michael Jackson never died.
He managed to convince Zed and got his job as Agent M.- Or maybe he just got kicked off the planet, or got tired of waiting and just went home.
The Liberty Island neuralizer had secondary effects built in.
Primarily, erasing undeveloped film and not having to look directly at the birdie (possibly not even having to be in the light itself, but only within a certain range which is lessened but not blocked by cement). It is likely that, aside from being lower-powered, the personal neuralizers are intentionally nerfed versions of this original-design neuralizer. Unfortunately, this means that any MIB agents within range who had their glasses off (anti-neuralizing field generators in the earpieces) lost their memories of that time as well, and that the MIB will have to find a new way to deal with flash memory storage for digital photographs now that it's become much more common.- The MIB doubtlessly wouldn't allow flash memory storage technology to be released to the masses until they already had a guaranteed way to alter it.
Serleena ate Scrad and Charlie.
The last we see of Scrad and Charlie is the fight scene in Jeeb's basement, where he says that Serleena was going to kick his ass if he failed to take down J & K. Now nothing in the ensuing fight scene implies that he died during it. So what might've happened is that after he lost the fight he returned and reported his failure to Serleena and she had a You Have Failed Me moment and devoured him/them. We already know that eating males is one of her preferred ways of killing them, so it's not too much of a stretch to say she did that to Scrad and Charlie. She's absent for a good chunk of the movie between Charlie's last appearance and her next scene, so she might've digested him/them by then, explaining why she didn't have a Balloon Belly like earlier. K was never supposed to get his memories back, but someone higher up made the writers change that.
A large segment of the movie is about K getting most of his memories back but very conveniently still forgetting stuff related to the plot. As a result very little is actually affected by K remembering his time with Men in Black, but the story makes more sense if he couldn't. His body still remembers, so K defeating a room full of aliens is still in the movie but K had no idea he could do that.This version of the story also means K doesn't have to be divorced because having a loving wife creates the conflict of whether he should return to being an agent or not. A part of him is happy to be a part of something grand again, but ultimately no force in the universe would be enough for him to leave her.
The fate of J's Non-K partners
- After the De-neuralizer is used the first time, and after the dust settled on the Evil Plan, all of J's previous partners were hunted down and restored. J was made to apologize to all of them. A couple My Fist Forgives You incidents take place, but Agent T thanks J; he is blissfully in love with the waitress that J nonchalantly set him up with, who, incidentally, is an alien in disguise.
- If the woman in the apartment in MIB 3 is the same person as the waitress (the character is played by the same actress) that would at least implicly confirm that T did in fact marry her and start a family, so the last part may be partially confirmed.
