I think his father is Jaern, personally.
Think about it. My theory is based off of Damian’s hair color, and the fact that Jaern shows regret when he says that he has to kill Damian.
As for the whole hair color thing, Audrey’s hair is white, Jaern’s hair is blonde, and Damian is a platinum blonde.
It’s just a theory, so please no overreactions!
Not really buying the whole hair color thing. A mixing of hair colors is incomplete dominance, but human hair generally uses a single hair color picked between both parents’ gene pools. Unless Damian dyed his hair (discounting the theory) or has a rare case (Kinda unlikely but possible considering how common people mix this up.)
Jaern regrets killing Damian most likely because he sees potential in him and that he has control over Shaymin. Damian doesn’t say anything hinting towards the fact while he was in full control of himself, but in the case of Audrey he tries to rescue her after being infected with Pokerus.
Audrey states that she left him behind, but I don’t recall her saying anything about the father. For all we know, the guy in the very first moments in the game at Telnor Town Hall could be his biological father remarried.
You would also probably think that the game would just state that plain and obvious if it were the case but shrug, what do I know.
The wiki description explicitly uses “stepmother” for the female parent in Telnor Town and “father” for the male parent in Telnor Town. That edit was made by a developer, so it’s a pretty good sign that his father is just the biological parent.