NieR Raid - Because I haven't seen anybody else mention it.
I haven't seen anybody else mention it yet, at least not in detail, but the reason it's so confusing is that fully appreciating everything requires not only knowledge of NieR: Automata and its predecessor, but Drakengard (at least 1 and 3, since Yoko Taro wasn't involved with 2) as well.
The first two bosses, the Knave of Hearts and Hansel and Gretel, are lifted to the original NieR. The semifinal boss lifted from Automata, where it served as the final boss and orchestrator of the plot. The actual final boss, on the other hand, has a lot of allusions to Drakengard: its subtitle translates from hex to "Aberration," but the DE code translates to "Grotesquerie." In the original Drakengard the Grotesqueries were... a race of extradimensional, giant babies with sets of adult teeth, that don't seem to have had any goal other than destroying the world. What set the NieR timeline into motion was ending "E" from Drakengard, where the protagonist Caim is drawn through a wormhole and fights the Queen Grotesquerie in the skies above Tokyo (1999 A.D., if I remember right); though he succeeds in defeating the thing it comes at the cost of his life, and the Queen Grotesquerie's corpse slowly infects the world with White Chlorination Syndrome. This leads to the Gestalt Project in an effort to save humanity, but this ultimately fails due to the actions of Nier; past that comes Automata.
Thus why, though it's in a digital space, we fight Her Inflorescence in the skies above Tokyo.
"Her Inflorescence" further refers to the flower from Drakengard 3 (which is a prequel to the original), the source of the setting's song magic. It was apparently created by the Grotesqueries (or Watchers, if you prefer) as a first effort in destroying the world, but is ultimately thwarted by the game's protagonist Zero (cold comfort, considering regardless of ending it leads to the original Drakengard). Her Inflorescence also wears Lunar Tears in her hair, referencing Kainé from NieR.
So yeah, even without doing the weekly "NG+" stuff I'm calling shenanigans.