So most crossovers I've seen with Danny Phantom and Kim Possible has Danny befriending or crushing on Kim who is either similar age or older. What if, however, you had Danny be of the same age as Shego?
We know that Shego was once a hero alongside her brothers and we can speculate it was in her teens up until she became an adult and got her degree for teaching. So what if in that time she met a fellow teenaged superhero that she could befriend and snark about teenage stuff with?
Easy scenario to set things up: the three vulture ghosts decide working for Vlad isn't so great so they quit and decide to work for Avarius, Team Go's bird themed villain. SheGo and her brothers have a hard time dealing with the ghosts until a certain white haired Phantom shows up after tracking them down. Danny and SheGo instantly bond and become friends with snarking as their love language. Danny crushes on her but tries t play it cool. SheGo teases him, though hides the fact she probably likes him, too.
They take turns visiting each other and hangout. SheGo (I'd probably have her real name be Sheila) becomes just as much part of the Fenton family as Tucker and Sam. Meanwhile at Go City HeGo doesn't necessarily like Danny because of his former bad reputation as public enemy number one, even though that label stopped being relevant after saving Amity Park numerous times.
Unfortunately, Danny and the Fenton's good influence isn't enough to dissuade SheGo from the pull of villainy and she suddenly disappears, ghosts (ha) both Danny and her brothers. Danny is heartbroken and feels somewhat betrayed; I haven't thought of the exact scenario and circumstances yet. He gets his degrees in engineering and starts working for a Dr. James Possible in Middleton. She goes full villain and starts working for Dr. Drakken.
Eventually, Drakken needs some tech that can only be found at one place: FentonWorks. SheGo tries to bow out but reluctantly goes in comes face to face with one Danny Phantom.
Phantom: Been a while, Shelly
SheGo: Spooky.
Drakken: I'm obviously missing something her; do you know him, SheGo?
SheGo; Dr. D, not now...