Yeah, I know what you were thinking when you saw that thread title. That doesn't even make sense! Nui was absorbed by Ragyo and that was the end of it, right?
I was a bit skeptical at first, too, but hear me out.

- Mako’s end credits outfit has the same colour scheme as Nui Harime’s dress, though upside down

- Her backpack is similar to Nui's eye patch

-- During her last rant, Mako talks about going on a date with Ryuko and kisses her twice, even though Mako hasn’t been that forward with her feelings for either Gamagori or Ryuko before then (since there's been hinting towards both ships). Who's the only person who's acted this way towards Ryuko before?

Nui, of course.
-On the ice cream, her eyes are blue (like Nui's) though Mako's eyes are brown

-Nui made a bunch of mon mignon prêt-à-porter clones, and we only saw the deaths of a few of them, assuming the rest had died as well.

Isn't it possible one got into Mako's body? (Or better yet, Nui herself got in, and what we thought was the original Nui being absorbed was actually a clone.) Their arms seem to posses reality bending abilities, so it's not too unlikely she could use them to take over Mako's body.

But wait, you say, wasn't Mako wearing her Goku uniform? Wouldn't it not work if Nui had taken her over? It's a reasonable argument, but Mako's body could have been used as a buffer so then Nui would be able to wear life fibers (which will make her much more deadly, since before she wasn't able to wear them since the life fibers in her own body were too strong).
Nui also had an intense hate of Mako, so it would make sense for her to take over her body out of everyone just to shut her up without killing her and enraging Ryuko even more. Plus, Mako is Ryuko's closest friend (and Satsuki's by extension), so Nui would easily be able to get closer to her two "sisters" this way.
Moving on,
-Mako keeps shutting the same eye that Nui has her eye patch on

-The end credits of episode 23 may have been foreshadowing towards Nui becoming Mako

-In the closing credits, Mako's hands are cut off in about the same place as Nui's (her hair is covering the actual wounds)


-This theory isn't too out there, since the creators have done similar plot-twists in other works

There were other parts to this theory, but they didn't work as well, so I chose to leave them out (such as Mako suddenly talking about fashion, and how they portrayed Mako as being the girl in the relationship, which Nui would definitely want.)

Is this theory really true? With the OVA in September give us answers? Or is Trigger just trolling everyone like with the "foreshadowing" about Mako's death? What do you guys think?

I've seen this theory around before, and to me it's really too much of a stretch. I have enough faith in what Trigger produced that they wouldn't ruin everything by pulling something this lame.

Besides,

Even when disguising herself as a unrelated male student, she's unable to get rid of her eyepatch and leaves it covered with hair. Her weird rainbow arms likely wouldn't be disguise-able either.

A likely story, coming from Trigger. I wouldn't delve too deep into it as I think at the end they were just referencing her because sudden death was sudden, but I can see where the deep thinking would come into play rather easily. I don't support this that much but I do see it.

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OH MY GOOOOOOOOOOOOOOOOOOOODDDDD!!!

I just...honestly hate this theory. It has a lot of holes in it and it seems that if it were canon it'd just be another cheap trick that TRIGGER would pull, similarly to how they killed off Senketsu just so the ending would be bittersweet and somebody would die, aside from Nui and Ragyo. Another reason is quoted below, originating from a conversation I had with a friend.

It's also like, yeah man I ship RyuNui and I love Nui, and yeah I know that technically the Mako=Nui theory would benefit my ship, but I also really love Mako and the Mako=Nui theory is bullshit and it seems like it was created just as a shitty excuse as to why Mako asked Ryuko on a date and kissed her just because "Nui liked Ryuko" like no what the fuck I know I'm digging my OTP's grave here but Mako showed hints of crushing on Ryuko long before Nui was even introduced.

But that's just the shipper in me talking. It's also that I don't think Nui is able to implant her consciousness in another person's, and as much as I hate to admit it, canon made it so Nui was devoted enough to Ragyo to kill herself without a second thought, so I doubt that she'd want to become the big bad after Ragyo kicked the bucket(I also think Nui's death was OOC but that's another story). Also, to be frank, Nui doesn't seem like the type to want to become the big bad, either, be her obsessed with Ragyo or not.

This reply probably seems a little scattered, but I haven't been able to focus on anything much lately. I just hope I got my point across, but most likely not, SO:

TL;DR: I utterly loathe this theory for multiple reasons, it doesn't make any sense to me, and did I mention how much I ABHOR this idiotic theory? Yes? Well, it needed to be repeated.