Long time ago, in the ancient times, mythical creatures of biological organic dominated the world from an unknown origin with powers beyond anything. These were known as Zoids. Ponies and mythical creatures in ancient times discovered them and through bonds between them, they live in harmony. However, those peaceful times come to an end when a necromancer names Grogar, plans to control the Zoids and destroy Equestria. To combat this, six chosen creatures, consist of Pony, Hippogriff, Yak, Dragon, Changeling, and Griffon were given six artifacts known as the Z-Fangs to connect themselves and the Zoids to fight Grogar, beginning an ancient war known as the Zoids War. Upon the aftermath, the Zoids have all but extinct after sealing Grogar into Tartarus. But Grogar use his dark magic to erase the bonds of all mythical creatures and the Zoids, thus the ancient times have all but faded and the Harmony of all creatures are all but divided, leading to events that yet to come.

Sometimes, in the future, Princess Twilight Sparkle opens the School of Friendship after the event of the Storm King Invasion in hope for her and her friends to spread the Magic of Friendship across the countries and other creatures.

Upon that, a wild orphan Earth Pony name, Spirit Howl attend upon after an encounter with Princess Celestia in Canterlot while stealing food from local markets, in hope for him to learn the Magic of Friendship but due to his wild nature born in the Everfree, he’s difficult for everyone to understand him. At one night, he encounter an ancient artifact leads him to a cavern and within, free an ancient beast name Wild Liger but at the same time, freeing Grogar’s army, the Death Army.

Now Spirit must find the other Z-Wielders and the other Zoids to fight back the Death Army, but when Twilight and her friends and Sandbar and his friends are involved, they had to work together to save their home and reconnect the lost bonds of the Zoids.