I am well aware right now all the people who watch me for Rhubarb are looking at this fic and asking WHAT IS THIS? It's my final story in my Danny Phantom/My Little Pony crossover trilogy. This story will make more sense if you read the prior two stories, The Phantom Pegasus and The Search for The Rogue Pony Prince. If you are not a DP fan, this won't make a whole lot of sense, period. Side warning: lots of DannyxSam coming in.
The secret that the best of the best Equestrian scientists were making a portal remained unknown to the rest of the citizens of the country. Leading the project were two scientists. Urged by their own children, they reluctantly labeled themselves as physicists rather than the paranormal experts they were. Princess Celestia granted them a home to move the portal into, away from the Apple Family Farm. Big Mac had once fell through it by accident. There was no unicorn to cast a spell on him to keep from being turned human by falling through. He was very freaked out for the rest of the day and night once he was helped back. Since then he had wanted the portal moved; it was no problem with the humans who resided on the other side. Big Mac just was afraid of it ever since that one incident. He steered clear of the cellar unless he had to go in to get something or put apple products down there.
Applejack personally thought it was hilarious in spite of how much it rocked her brother. It almost inspired Apple Bloom to run through the portal just out of curiosity, but was prevented by her siblings. The first incident with Big Mac was enough for the Fenton family to consider looking into a different spot for the portal. This consideration was pushed when a certain Cutie Mark Crusader almost decided to go exploring in it.
So Celestia offered the Fenton family a home in Canterlot. Instead, they asked for a house in Ponyville instead; somewhere closer to friends. She agreed, and financed their moving into a home there. With much effort from both Celestia and Twilight Sparkle, the portal from the farm was moved to the basement of the Ponyville home. Maddie and Jack were already setting up a second lab.
Jazz did her best to steer her parents clear of an ostentatious house, begging them to have "one place of normalcy." Jack was disappointed in particular. Mr. Fenton wanted to show his work to Equestria, but he wasn't even allowed to put up a giant neon sign that said FENTONWORKS. He was going to anyways until Maddie coaxed him into not doing it. She claimed it would serve as an inconspicuous front for the building of the portal with the other Equestrian scientists. Said scientists were the only ones along with the Fenton family, Sam, Tucker, and a certain six ponies who knew the true colors of the family.
Maddie had told him that it would make a good place to experiment in utter privacy, and that nopony would suspect a thing. There was always the worry a ghost would attack and Danny would be forced to go ghost, and everypony would learn about a superhero named Danny Phantom. Nopony would suspect a thing about young Danny Fenton, quiet son of Ponyville physicists.
Rarity could sense Jack's disappointment and offered to help decorate the house. She picked out furniture and decor for the home that made it look beautiful. Even Jack had to admit that it was nice, even with a few less things he enjoyed about Fentonworks. Nopony found it odd about them when they moved in; just a nice family of ponies moving into Ponyville. And although they were already friends with Pinkie Pie and not strangers to the town at all, Pinkie couldn't help herself. She gave the welcome wagon, literally. That particular event left them covered in cake from the wagon.
Danny, Sam, Tucker, and Jazz befriended some other ponies their age in town. Jazz herself would often go to Twilight's library if she had spare time and would either read or have Twilight teach her a magic spell or two. The two bonded quickly and became very good friends when they both loved reading and learning. Danny would sometimes help the other pegasi with the weather if they needed extra help. At first, this was not in his jurisdiction; when Rainbow Dash needed help, she made him come help. Of course, when the boy learned that he could stand on clouds without falling through, he didn't mind helping at all. He found it to be fun. If he wanted to be alone, sometimes he would simply lounge on a cloud...until Rainbow playfully kicked him off of it.
Sam and Tucker would enjoy the town, too. It served as a place of refuge from the ghosts that constantly invaded Amity Park. The vast majority of the time they stayed on Earth, waiting to take care of ghost attacks, go to school, and do homework. Perhaps take a visit to the Nasty Burger, even. But if they needed to relax or they wanted to visit friends, they knew where to go.
This went on for a few months. Every couple of days Maddie and Jack would take a trip up to Canterlot to supervise the building of the portal. One day it was finished, ON button in place and everything. The majority of the engineers behind the portal avoided that particular button like the plague the entire time while making it. It took the bravest of the scientists to be the one to install it while everypony else stood outside and stared.
Once the portal was complete, they decided to build something else to improve security. That was a magic lock to hold the portal closed so tightly nothing could get through unless opened by only those authorized. Twilight Sparkle was asked to help with it. By this point, the others wanted to see how the inside of the portal looked before being turned on, and so they were invited to tour it.
That was when everything peaceful fell apart again and yet another adventure would begin.