I mean he wakes up from nightmares, one where he microwaves one of the dicks, where mio seams to know something, he wakes up from a pre tomoki fight, i'm not 100% but I think there was another one too. he goes to tomo, who says she doesn't see anything which shouldn't be possible, but looking back on everything that happened, at least after the dreams started to happen, certain things make more sense if they had some idea of what went on before. if that is the case, it explains why that entity did not give makoto something, as he already got what he wanted, a second chance, it also explains some of mio and tomos actions, and can tie into some other things. The thing is, even if things in the story contradict this unless the story gets told from pov from a god that may know, they are able to tell makoto pretty much anything they want and wash it away.