Happened....happened is the past tense of happen. Happen one of the simple present forms so you can not use it correctly in this sentence. The exception is when you use the word did. What happened yesterday? What did happen yesterday?

"What happened yesterday?" is the most natural. However, you can say "What did happen yesterday?" when you want to emphasize the question to get more specific information. "What REALLY happened yesterday?" is the same as "What DID happen yesterday?" You need to emphasize the word "did". This is natural and very common too.

"What happened yesterday?" is what you need.

It is more native to say: "What happened yesterday?"