Random thought about this:
When Father and Neb switch places because of Negative Numbuh Four, Neb has to do his best Father impression to make people, who don't immediately cower at the sight of him, listen to him and keep from getting bodied by the other villains. It works for some of the villains, but others start picking up on it somehow, which is how Neb finds out about Faust. Nigel practically wields her absence as a weapon, telling them that she's on her way back and will trounce them the moment she finds out they messed with "Father" when he wasn't "feeling well."
This causes Neb to be absolutely TERRIFIED of Faust, wondering what she's going to do to him when she realizes he's not Father upon her return. Nigel tries to tell him she's not like that, but pauses when he remembers she hates other adults and doesn't know how she would really react to this. He flat out tells Neb that there was a real possibility that Faust might kill him before he's elbowed by Numbuh Five.
When Faust does return to the Delightful Mansion, Neb does his best to avoid her and not make eye contact, which makes her think he's still pissy that she didn't go with him to the spa. Neb immediately gives himself away when he thinks she's getting upset with him, apologizing profusely for something he had no idea of. Faust just stares at him and the next thing Neb knows he's pinned to the wall by several sharp icicles and with two ice blade katanas criss-crossed around his throat, held by Faust who started threatening him, asking who the hell he is and where Ben was. He RARELY apologizes right off the bat.
Neb word vomits the whole situation and bursts into tears, asking her not to kill him. This makes Faust pull away and the icicles disappear in a frosty white cloud. She agrees to help, mainly to get Ben back, but also because Neb makes her uncomfortable with how wishy-washy he is.
While all of this was going on, Negative Numbuh Four was gathering strength by telling the villains about how his world is and how they could replicate it in theirs. He was part of the reason some of the villains started to turn on "Father," believing they would eliminate Neb for him, the only ties left to the other world. He just wasn't aware that Father had a partner in this world that scared the bejeezus out of adults.
Neb's lack of a spine, especially around Negative Numbuh Four, does irritate Faust to the point that she starts to softly rage-bait him enough where he won't give into emotions immediately while Sector V and the Delightful Children fight the new threat. She uses his tender spots against him to light a fire under him and make him stand up for what he needs to do. "What if Ben reverses the progress made and makes the other side worse while you're gone?" "Ben is a nightmare for all children, are you willing to let him do that to your world?" "What about your kids?" "What kind of father can't protect his kids from dangerous people?" "Aren't you tired of being walked all over? Don't you just want to go Rainbow Monkey-droppings?"
Neb snaps and ends up finding that he does have abilities of his own, but rather than fire, it's the opposite. Water. This scares Negative Numbuh Four into surrendering, of course, only after he was caught in several whirlpools and being tossed around by an angry mini sea. Neb snatches Negative Numbuh Four by the ear and drags him back toward the spa with Sector V and Faust in tow. The Delightful Children stayed behind to put the other villains in their place and prepare for their father's arrival.
Now all that was left was removing Father from the Negative world.
