It being an in-universe movie doesn't prevent it from being the same universe. That doesn't really seem any different than when it happens in the View Ansewinverse, Doctor Who, Die Hard (due to the crossover with Chuck), and probably many many more.
I mean, they got Vincent D'Onofrio back for the series. I've been told that they reference K being neuralyzed in the past from someone who has seen the series and told me it can work.
The Men in Black wiki finds no issues with L being there. In fact, it makes sense that she works for MiB since she joined in the first film. I'm not sure what they could be talking about, but considering the actual wiki finds no issues with Agent L, I'm inclined to believe that her being there longer than Agent J is an inference they made rather than a fact. Even still, that's not impossible considering that she could have been retired before the first film anyway.
—Agent L Agent L, originally Dr. Laurel Weaver, also called Elle, or just L, was an agent of the MiB. She was a beautiful but cynical former deputy medical examiner. She joined MiB after Agent K was neuralyzed, so she became Agent J's new partner but later became chief scientific officer and an...
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