She cares for him a whole lot, even if nobody else would. Including himself. She has nothing but unconditional pure love for a lost soul who's trapped underneath a sea of lies. She's not immune to it, far from it. It's really difficult to ignore his creepiness. But unlike everybody else, she stayed with him despite his horribleness; she didn't hold any grudges for his mistakes, and encouraged his docile, friendlier side.
Anybody in her position would have more than enough on their plate to justify shutting him out, leaving him behind. He admitted that while he is deeply sorry for his actions, he believes that he does not deserve to be forgiven. That he'd rather die again, instead of having to live with the thought that he failed her.
And yet she remains unwavering. From the moment they met, through their deaths, and finally as sprites, she effortlessly tapped into the mightiest muscle of all. The heart. He did do his best at disappointing most everyone, and cornering himself into a pocket-dimension of eternal sadness, where nobody can find him. But she's connected to him on an entirely different level. No cosmic force or spacetime law or metanarrative bullshit can separate it.
Neither of them play too big of a part in the universe. Or so it seems. But even the big lipped bastard himself admitted that because of their connection, it's difficult to entirely get rid of them. Nepeta's commitment to Equius had survived hell itself, metaphorically speaking; the hemocaste, the author, the VOID, their deaths, several lifetimes in the afterlife, a retcon, sprite-ification. It even inspired others to emulate them, and I'd say it influenced the Alpha universe very deeply too.
Without a doubt Nepeta's love is the purest thing in the entirety of known fictional universes.