Here is my theory dump about Kaori, John, Sekai, and the Wire God. This post is very long, so proceed at your own risk. (And sorry if I'm repeating any old analysis here, but it's really difficult to search an 1850-page thread for discussion of old events.)
tl;dr: The Wire God possesses the largest cock in Kumon-mi and has been using it to dominate Sekai.
Really good run down, it's always nice to see things more focused like this.
As for the disappearance of USER2, it's probably less a disappearance and more it being impeded. In that 'Såsom i en Spegel' Chapter 2 Kaori event, after something messes with John, Sensei not only loses the ability to communicate with him, but USER2 also goes offline at the end of the event, even though it's still Winter:
(The ending is cut off in replays)
It likely was still around, with even Noodles doing reconnaissance for it:
In Chapter 3 during Beachmas, in the 'Fetch Quest' Main Event.
But, It wouldn't be until Tsuneyo's 'TH15 15NT M3' in Chapter 4, that USER2 seemed to "claw itself out":
Then Sensei ends up smiling, Tsuneyo blacks out, Sensei pisses himself, and eventually USER2 and Pareidolia fight over Sensei and Nao-chan entering that door last update. Now, here we are.
Also just to point this out, Tsuneyo's father loves trees:
And, so does Sensei, and Sekai it seems:
SeKaori showed up after Kaori went to where the trees live:
It's also paper which led her there, and to Nao-chan, which is also what recently led them to the woods where they ran into Sensei (Yuki, etc), and eventually to the door that USER2 wanted Sensei to open last update.
Overall: I'm not sure if USER2 is trying to protect Kaori from SeKaori, as it kind of seems like it's behind it, or at least has something to do with it. Of course that's just a theory.
