>>149214614 (OP)Rereading the mind cage chapter, it does feel like there are unresolved mysteries. There is the curious mention of Tony's mind being separate from his body, just like what Kat has now done to Omega.
Tony's weird affliction has always felt very unnatural, so perhaps his mind was somehow altered. Maybe Omega had something to do with that, in order to bring about the events leading to the Annie-anomaly? I kinda doubt it, though. Every part of the comic up until the distortion was essentially planned by Omega, so Omega could always be the explanation for everything, but it feels like she isn't behind this one.
Either way, I still kinda believe in Tom's ability to tie it all together in the end in a satisfying conclusion.