Taking what Ella says when you first meet her with his friends if you select "Do we know each other?" she says she has seen the MC around before.
Yeah, but that really doesn't explain calling him by his first name when she knows pretty much all of his friends, something we find out later when snooping around her house when we find a list with names there... So why would she greet MC by his name and greet the others there with "hi guys" when they're on that same list? Very simple, Ella has been closer to MC than the others, and not just observing but interacting.
The above scenario is far more likely than it being because she killed his mom or took over his dad and replaced him, heck if I remember right she even admits that she was watching MC for a while now in her apartment
Again, there's no info in the game that suggests Ella killed MC's mother. But that does not mean she did not kill her either.
It's a theory, we know the mother was killed, MC was attacked in the same incident and needed eye surgery and has scars around his eyes. Perhaps a monster attack? It would fit the theme of the game. Your father knows what happened, you were there but don't remember and your father will not answer your questions about the event.
MC's father has the habit of disappearing for months, Ella has a similar history.
MC's father pulled strings to get MC in the college that happens to be where HERO base is...
Ella infects MC, Jake, Kenny, and Michael all students of said school... Alice and Tiffany, the daughter of a HERO leader just "happen" to be there too... And Jared the son of the competion aswell...
MC being a student there is convenient for Ella, however it's unclear what purpose it would serve for his father.
Ella knows about MC fighting Kenny and apparently MC's father transferred MC to a private clinic after the fight...
MC's father just happens to pop up several times that just seem too convenient.... Short after the infection but also you investigate the stripclub together... Also Dexter knows your father....
So your father knows about superhumans, gets you into a school that's above a superhuman base and seems to be off radar except for some convenient (possibly?) coincidental moments around crucial events in the story...
MC's father being an alter ego of (or shape used by) Ella seems to be a possibility, but your father using you as bait to catch Ella is another one... (Brianna's inspector being Ella would fit there) But it's all just too connected to be just a coincidence...