in NG+ he was sent to many schools because Haruhi (and the author) did not like him, including sending him to an All-Girls school in a girl uniform, a 'delinquent' school, to USA and lastly to Xavier's.
and Mikuru (both) was involved in a series of 'embarassing' incidents and accidents so Kyon wouldn't find her 'cute'
in that fic Itsuki and Mikuru were bashed needlessy because no freaking one but Haruhi herself would know thst something changed in the timeline as she 'rescued' Yuki from the IDSE way before the series, the SOS doesn't even exist and even then she forced Kyon to join Nagato's club and so she didn0t form SOS, the only threat to her could be itsuki's link to the organization (a stupid reason because they want haruhi happy, unless you go by the whole Secret Evil Organization whose goal is controlling Haruhi, like Itsuki did in Downfall, where he was the main antagonist) and in the case of Mikuru it's part utter Jealousy and sees her as a threat, well here is the quote:
"Anyway, we're a package deal. And trust me, you won't find any manipulative busty time-traveler nearly as cute or moe as her!"
"It's a good thing I was carrying that around for the drama club supplies!" the green-haired girl chortled. "Haha! Mikuru-chan, what were you even doing crawling around, peeking underneath that bush, nyoro?"
"I-- This," the mysterious ink-covered 'Mikuru' whimpered before subsiding into sobs.
"Sorry!" someone called from inside the building. "It slipped from my hands, honest!"
The green-haired girl cackled again, before putting her phone in her pocket. "Let's get you cleaned up!" she cheered. "Don't worry, I edited out the parts where your face could be seen before I put it on the web!"
Wailing, the ink-stained upperclassman allowed herself to be led away by her chortling friend.
and the incident with Older Mikuru and the Flour.
that Haruhi comes as utter Petty, basically replacing Nagato with her 'pet', makes a runing gag out of Koizumi and continuously humilliates Mikuru so she doesn't meet Kyon.
that IS bashing, slight, light bashing.
it's like a lot more sane CED!Naruto with his sense of ethics and morality still hanging.