Launching right into this with a quick warning that there are spoilers through today’s final episode, as well as a single (rather large) fact revealed on Reddit but not included in the podcast.
The big important fact that was revealed on Reddit, but wholly omitted from the podcast, is that Adnan told his attorney that (a) Jay was cheating on Stephanie; (b) Hae found out about it, and (c) Hae said she was going to confront Jay about it. This gives Jay MAJOR motive, especially considering the numerous times we’ve been told that Jay would do anything to protect Stephanie.
So here’s my theory: Jay and Adnan killed her together, in the parking lot after school. One of them (probably Jay) stood watch to make sure they weren’t seen while the other (probably Adnan) strangled her in the back seat of the car. I’m thinking maybe Jay played on Adnan’s feelings and manipulated him into doing it to silence Hae. After the fact, Jay got nervous about getting caught, and went to the police. I suspect he told Stephanie that he knew Adnan did it, and Stephanie coached him to go—but that’s totally just my own guess, there’s not much evidence of that.
Anyway… So Jay needed to put some distance between himself and the murder so he wouldn’t seem as guilty as Adnan, which is why he made up the phone call scenario. That way Adnan was the murderer, and Jay was just accessory after the fact, not an accomplice. I don’t know whether he figured that out himself, or if the cops coached him so he could get his plea, but either way that’s why the phone call nonsense, when in fact they were together the whole time.
Adnan knows all this, but he could never finger Jay, or even hint at any knowledge, because his attorney’s strategy was to deny any involvement and insist he knew nothing about any of this. He’s stuck to that story of his innocence ever since, and people (and the show) make a big deal about that, but notice that his current appeal is entirely based on the fact that he now says he wanted to plead guilty fifteen years ago.
So that’s my theory. I think it holds together quite well, including the little bit of new evidence that was revealed in this last episode.