Ella has some idea that something is going to possess or fuse with the MC, but I don't think she knows about the Eye specifically. Early in the game, right before she fights Clark and Lexi, the narration describes her inner monologue musing about her plans. Apparently she's looking for a host body for some entity to occupy, and is sad to think that the MC is the probably the best bet for that. But she doesn't appear to have any awareness of what exactly that entity is. She seems to think that potentially it could find a host in any strong enough superhuman, regardless of their monster parentage. The Eye, as far as we know, has a particular connection to the MC and the Third and Fourth Apostles. Which makes the Eye even more mysterious and terrifying, to me. It's convinced Ella that she should work towards its arrival, but without actually telling her anything about what it is.