Toko had never been a fan of Makoto, even before Junko took away their memories of being at Hope's Peak...or so she's heard; those memories have not returned and she doubts they ever will. But the memories she does have aren't ones that paint the other girl in a good light.
When they were still "trapped" in Hope's Peak and forced to participate in the First Killing Game, Makoto made a point to hang out with her, even when it obviously made them both uncomfortable and anxious and "reinforced" Toko's suspicions that Makoto was trying to get her to let her guard down so she could swoop in and steal Master Byakuya for herself. Needless to say, once Makoto and Master Byakuya did get together (in reality, back together, as they would all later find out) both Toko and Jack went beserk; but Jack actually attempted to kill Makoto whereas Toko merely resorted to cursing Makoto's name more than usual.
But this, this, was more unpleasant than any of that. By this point Toko had mostly gotten over Byakuya and had begun an iffy relationship with Aoi (of all people) and was good friends with Makoto's younger sister, Komaru. And yet here Makoto was, apologizing to her for not being able to keep her own boyfriend alive.
Toko has no idea how Byakuya ended up going to Makoto's trial in place of Kyoko but she understands why he went and why he chose to keep his forbidden action a secret from Makoto.
Passing the fourth time limit with Makoto Naegi alive.
She also understands that Makoto knows why Byakuya didn't tell her the truth about his forbidden action (apparently passing it off as not being able to speak directly to Aoi) and she understands why Makoto is apologizing to her. It's likely she'd done the same with Kyoko, Aoi and the Occult Idiot a while ago but only now is getting around to Toko because she and Komaru were held up in Towa City for a bit longer than anticipated.
Maybe it's due to her friendship with Komaru that possesses her to act in such a way, but for whatever reason Toko surges forward and hugs the poor girl before either of them even realize what she's done.
Makoto immediately goes stiff out of shock and confusion, and perhaps a bit of fear. Toko herself is feeling quite awkward but pats the shorter haired girl's back in a manner she hopes is comforting. "It's okay, Makoto. You did everything you could." It's probably not the first time Makoto's heard those words and probably not what the other brunette needed to hear (Toko is the Ultimate Writing Prodigy; surely she can come up with something better than that, goddamn it!), but Toko has never been good at interacting with Makoto, so can you really blame her for being out of her depth?
But Makoto relaxes and hesitantly returns Toko's awkward hug - as if she's scared Toko will sneeze any moment and Genocide Jack will attempt to disembowel her again. "Thanks, Toko."
A/N: Well, that's one request started. I'll admit, I was interested in Munaegi prior to getting this request, I couldn't really think of a decent plot for a fix. Thanks to Shiranai Atsune for making this request! Sorry I couldn't get it out sooner, I've been a lot busier than I thought I'd be. I'm also working on some of your other requests, so don't worry!
If you're curious as to why I paired Toko with Aoi (of all people) instead of Komaru...They got together before Ultra Despair Girls and Komaru has a crush on Yuta (who survives in this universe). I suppose that's not an actual reason, but don't think I really have one. It always just seemed like an interesting pairing to me with how Toko seemed to go out of her way to make Aoi blush sometimes.
And about Toko's behavior; obviously she and Makoto would've had an even more strained relationship if Makoto was a girl, especially if she "lost" Byakuya to Makoto twice. But I'd like to think Toko is the type who doesn't try to steal (or "steal back") other girl's boyfriends and even in canon Toko is shown to begrudgingly respect Makoto after the first game. I also want to create an incredibly obvious difference between Makoto's circumstances and Munakata's (as if they weren't already obviously different).
Have a nice day!