Since it seems you all like theories so much, let me regale with one of my own: At the very bottom of the Abyss, there's Bondrewd. He's the creator of the Abyss, the one original true resident.

I know it sounds ridiculous, but think about it. We know that he's basically immortal at this point, because he's more of some bizzare parasitical entity than human. We also know that he's scientific genius obsessed with the Abyss. And we know that there are Relics capable of manipulating with time, too. So there's nothing that would make it impossible for Bondrewd to obtain a Relic enabling him to travel through time and somehow creating the Abyss in the process.

Also, have in mind that Tsukushi loves to psychologically torture Nanachi. And what would be more horrible experience for her than seeing Bondrewd torture her friends once again?