>>8268332The obvious ones are based on the two "famous" characters from the tv series
>>8264273>Drekk The alien serial killer has escaped to earth and now a couple new agents have to figure out who his targets are and stop him from killing them. (no cat macguffin means it's a similar "feel" to the original without being the same story, which is what a reboot is usually looking for - plus questioning his known accomplices / witnesses / etc is room for shenanigans)
>>8264267>AlphaThe new agents uncover a shameful secret in the MiB's past that forces the old agents to come to terms with some ancient sins and cover ups etc. - Alpha is back and he's targeting (whoever) and the agents must protect them. (again, for reboot purposes it's a similar story to both MiB 2 and International, except instead of the weird and forced sudden betrayal turncoat shit in the third act of international, it's actually focused on exploring the agency through the eyes of the new agent and the MiB's history (/old agent's past), again, serving as a reintroduction for the reboot).
On a personal note, I liked cartoon L being the ultimate straight man to J and K and the Worms (and even Z), but they got rid of her in the sequels. If you wanted to go in a slightly more original path, go with L uncovering the mystery and conspiracy of the MiB and her joining as a subplot while the two agents deal with Alpha/Drekk, (which they started to do with international as the main plot... and then abandoned about half an hour in to do the "amnesia + which good guy is really the bad guy" plot).
If you're not looking for reboot stories, though, a lot of the MiB cartoon episodes dealt with alien tech falling into the wrong hands or being released into the general public, or alien prisoners/politics/shapeshifter shenanigans. That's before you hit the X-Files nostalgia train and try to do a male/female team of agents investigating weird shit route + James bond spy gadgets.