After the second Death Star was destroyed, peace finally came to Equestria. A new foe now rises from the shadows and Charming Thunder and Twilight must work together to save the balance of Equestria.
After a fierce battle at Canterlot and the Death Star was destroyed, half of the Lunar forces remain vigilant across the land of Equestria and has brought back to life the dark unicorn king of the Crystal Empire.
An old Crystal Knight from a thousand years has returned and he now seeks revenge on Discord. Charming Thunder must protect Twilight and his daughter, Light Sparkle, from his wrath.
War is coming once again to the land of Equestria. The Phantom Consortium once led by Dusk has been taken over by Lightning Dust. Charming Thunder and the princesses plan to stop her with the help of their former leader; Danny Eclipse.
Charming Thunder's spirit visits Twilight and her student; Luster Dawn, for the first time in many years since Twilight became the new ruler of Equestria with her son; Starshine Sparkle.
After Harkon's defeat, Charming Thunder's brother; Danny had his memory wiped from his recent strike. Charming Thunder and his friends search for him while a new threat rises from the vines of Discord's plunder seeds.
With Charming Thunder gone for three years, Twivine hunts him down while Starlight leads a search team with the help of the princesses. The situation changes after finding out that a droid carries a map to his location.
During a congress meeting, Danny has sensed a change of balance and has informed everyone that Havoc and Arthas have returned. Danny and Twilight will be dealing with Havoc while Charming Thunder will take on the Lich King.
With the defeat of Malgus and his empire, Charming Thunder along with Starswirl the Bearded brought back the Crystal Knights. Now the essence of Nightmare Moon returns and posseses Charming Thunder and plots her revenge.
Light Sparkle wishes to join the Crystal Knights but Charming Thunder refuses for her to join. Ever since the fall of Regal Crescent, Princess Celestia senses a dark presence that has emerged from the shadows.
The Lunar Republic has returned with the help of Cyber Eclipse who was Danny. With the power of the ancient weapon the Dark Forge, they will use it to revive Mephiles the Dark and spread darkness across the land of Equestria.
While King Cosmos and Queen Galaxia secretly prepare a ritual to revive Danny, Charming Thunder has to deal with a rebellion that has emerged in Equestria led by a stallion named Zero.
The time has come to fight Mephiles and his alliance. Charming Thunder and his new allies must stand together and put an end to the war once and for all.