Continues right after Chrysalis is expelled, Celestia, and a few of the Mane Six begin to find things that quickly generate a conspiracy altogether about HOW the Changeling Queen could have caught wind of the wedding, and how to infiltrate it without being discovered.
For a while, Celestia is given false prophets, and demands, such as her giving up the crown, and the throne. While she refuses, she also neglects to take the entire situation too seriously... as she believes Chrysalis was the biggest threat, and denies the possibility of something far greater looming over her head. Despite this she intends to go on with the daily life, and ultimately get to the medal Ceremony dedicated to Shining Armor for so many years of Captain's duty. The ceremony takes place only a few weeks after the wedding.
However it becomes apparent that that is not true. As the reader is completely aware of a Dark Entity who calls itself "The Dark Soveriegn" or "Dark Soveriegn" "Lord Sovereign", and so on. He is the true entity of evil. Instead of love, he feeds of negative emotion like hate, jealousy, and misery. However, he lacks Chaos, as Choas itself is a neutral foe... seeing as in the series, Chocolate Rain, and Cotton Candy clouds are not exactly true bouts of the darkest will.
Umek/Dark Sovereign turns out to have a very old room inside Canterlot Palace, which Rainbow Dash, and Fluttershy discover, giving the reader time to assume he has lived in Canterlot before... many many years ago, as the place is entirely ruined. The reader learns that the day this occurs, the ceremony is only hours away.
While everyone is assumed to be present with Shining Armor(And Cadence as well) In Ceremony Plaza... Pinkie Pie is the only pony to be late... she is wandering about Canterlot with her own innocent mischief, and planned to be just on queue for when the activity started. She is cut short by a twitch in her cutie mark, something she has never felt before... she can only assume something terrible is about to happen, and rushes to the PAlace.
You learn this is correct, as at one of the less important entrences to Canterlot, is not as heavily guarded. an OC whom you meet earlier in the story, Solster Fire, distracts the guards away from the gate, and leads them off... to hit them with a sleeping bomb... knocking them unconcious, and allowing two other OCs Black Knight, an Scare Crow, two mercenary Zebra's one having an intense grudge on Shining Armor for a reason that is not admitted until early in part 2. They open the gates, and Black Knight dispatches rather easily, the last colt of the gate guards, implying he has a record for being incredibly efficient in combat. HE has a magical weapon that is not revealed until part 2
It is with the act of these three equines, that Dark Sovereign is able to waltz through Canterot like an average citizen despite being nearly as tall as Celestia... he stands out, yet he appears as an ancient, and weak old man... He is accumpanied by Twilight's rival... The Great and Powerful Trixie, who has alligned herself with Sovereign in order to show ALL of Equestria she is stronger than Twilight Sparkle... she is also earlier in the story.
When they enter Canterlot palace, the guards have already been quietly dispatched where need be... and Sovereign merely walks in... he ressurects the numerous statues in the grand hall... creating a small army of tough moving stone ponies. And finally interupts the Medal Ceremony even while Pinkie Pie tries o warn everyone of the impending doom.
The story cuts out at "Welcome Home", and immediately jumps to part 2
Chrysalis has a more major part in the second part, Part 2
