I broke this down into an even more simplistic three act structure: I have found its helpful for me to describe the plot as generically as possible in order to do this, otherwise I will overthink it.

In my mind, Act 1 is just Kay's call to adventure. His multiple encounters with the unnatural world and with Jay are a call for him to make a decision. The end of the first act is when he makes that decision and says, Heck yeah, I'll join in!

The second act begins when Kay and the audience are fully introduced to the world Kay just joined by watching the two of them on the job, and through the introduction of the McGuffin, the villain, or the mystery. We ride along with Jay and Kay as they have various adventures and see what its like to be an MIB. The end of Act 2 is when the mystery is solved, the McGuffin is obtained, the villain is cornered, or a new threat is introduced. In this case, when the other aliens show up to destroy the Earth is the end of Act 2.

Act 3 is the final confrontation with the villain or attempt to keep or procure the McGuffin in order to save the planet. At some point it looks like the protagonists might lose but then rallies and wins. This is the third act. The third act ends when Jay announces his retirement.

Everything after that is epilogue.