Elias Mannix doesn’t exist now. Just like you can’t explain which came first, the egg or the chicken, you can’t explain how Elias Mannix was born. This is called The Bootstrap Paradox, where you don’t know how all of this started. The movie “Predestination” is also based on this theory, and the movie takes this theory to the next level.
My theory is that someone in the future time-traveled to the past and did something that resulted in Elias being born. Just like in the series, no one loves Elias, so he makes a plan in the future to time travel to 1889 and start his own family. In the series, Elias really loved Polly (Hillinghead’s daughter); he always wanted to stay with her. This resulted in him being in this loop forever.
Hillinghead put the idea that no one will love him or care about him. From that day, Elias starts thinking about that every day, which disrupts the relationship between Polly and Elias. Polly starts suspecting him and soon finds out that Elias killed her father. Polly finds out about Elias very soon; in the original loop, Polly finds out about Elias after their child is born.
Their relationship is very good, and Polly always cares about Elias. Polly’s love was the reason why Elias wanted to be in that loop as no one loved him from childhood. In 1941, he recorded a secret audio that told Elias not to activate the bomb. Young Elias Mannix didn’t do anything in 2023, and the loop broke. Elias was erased from the timeline and all of the things he did.