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I never really understood this.
Jeffrey Sinclair disappeared after Season 1 due to the actor departing the show. When he returned it was as a Minbari.
The predestination time travel paradox and him becoming a different species never made sense to me.
Can anyone give an explanation?
He did not reappear as a Minbari. He came back as his original human self. He did not change into a Minbari until 3x16 - 3x17, the "War Without End" two-parter.
They were the ones that caused the disappearance of Babylon 4, and took it back 1000 years into the past to use as a base in the last Shadow war. During the journey back in time, he used a Triluminary from the Great Machine to become Minbari, which would later become the same one Delenn had used to become human. He became Valen, a Minbari not born of Minbar.
He was human with a Minbari soul. It's a bit of a paradox but stable, it requires a closed time loop that can't change and has no initial beginning. He went back in time and merged human and minbari, causing minbari souls to be born to humans, which caused him to exist, which caused him to be able to go back and become Valen, closing the loop.
Ohare left the show on an ending the season agreement due to increasing effects of mental illness that eventually claimed him in 2010 or 2011. It is said to have not been preplanned.
There's some more information here.
And a quote from the same article;
In 2012, Michael O'Hare, who played the original Commander of Babylon 5, Jeffrey Sinclair, passed away. During his life, however, fans were unaware of the fact that he suffered from delusions and paranoia due to mental illness.
That was the real reason he left the show after only one season. Straczynski explained how O'Hare struggled, how he was barely able to come back for a two-parter to close his character's story, but above all, that O'Hare wanted people to know the truth after his death.
There was a device found on the planet that B5 orbeted. He used this device to change himself into a Minbari. Delenn also used a similar device to change herself into a half Human half Minbari hybrid. Also found on this planet were the time warp devices Sinclair and the other B5 crew used to travel though time.
