I'm shocked I didn't come up with this sooner. MLPXDP
Ancient of Space Danny, with him having fully ascended years ago with his Dimension pretty much dying out after the years have passed. Clockwork has a Mission for him, and something Danny was expecting, since he felt the Birth of Two-New-Space-Adjacent Beings.
So he goes to Equestria, LONG before anything has even happened. Where he finds the Fillies, Celestia and Luna before they were even 3ft tall and hiding in a cave. They were obviously freaked out, at seeing the massive Alicorn before them - before Danny gently calms them down.
Yeah, that's right. Parent Danny, with CELESTIA AND LUNA as his adopted kids! Runs in the genes.
Point is, Danny helps them and guides them - but he does NOT get invovled with big-historical-events and makes sure to stay hidden. Considering his thousands of years being dead, that's easy.
He's avoided being in History Books, Celestia and Luna never mentioned or alluded to him, he was simply there to guide them and help them. But he also made one thing, very clear to Tia and Lulu.
There are things he absolutely cannot interfere in or help with. He learnt that from Clockwork years ago, and neither of them truly understood what that meant.
Until Luna turned into Nightmare Moon.
When Danny finally showed up again after her Banishment, Celestia cried and asked why Danny didn't do anything. Why he didn't help her. But Celestia took one look at his eyes, eyes full of sorrow.
And that's when she understood.
And all Celestia could do was cry in her adopted Father's hooves.
And this would also explain why Celestia doesn't do much in the show, because her Father taught her to trust in her own choices and have belief. And of course, know that there are some things she cannot interfere in.
^-^
Years passed, and while Danny does show up every now and again - Celestia has been seeing him less and less, only because he's gotten busy and because, she's learned all that she could from him, without spoiling too much.
So when Nightmare Moon returns, when Luna is reformed - Discord too, and her student becoming an Alicorn, Cadence having her baby ... things were going great.
Until Celestia and Luna recieved a Sticky-Note during breakfast. But when reading, both Sisters nearly choked on their foods and started panicking like little fillies all over again.
King Phantom was coming to visit.