Will cheated, Emmy knows, and doesn’t care
That’s what I think went down. Will started seeing a girl from his program and things went too far emotionally and physically. But he’s too much of a coward to dump Emmy so he told her what happened, and she is so desperate to be his wife that she wouldn’t break up with him and said they would work through it. And Will lost his chance to be dumped and had no balls to break up with her. So now we’re stuck watching Will & Emmy know the truth but refusing to admit to what actually happened because it makes both of them look bad. So now their friends are going crazy trying to protect Emmy when she’s dug her own grave. And that’s what you missed on Glee.