The Rise of Lord Naturus, aka the Tree of Harmony

"If we are going to defeat Naturus, I need to get to the Tree of Harmony, even though Naturus seems completely immune to magic at this point, maybe the Tree's magic can negate his immunity to magic." Twilight said to herself, pacing back and forth. "If I need to defeat him, I'll need all the help I can get!" Twilight began to write letters to her friends. Whatever Naturus was, he was even stronger than the Princesses in sheer power, and almost killed her brother and sister-in-law. Without Spike, she was forced to write it by herself.

Dear Applejack, Fluttershy, Pinkie Pie, Rarity, and Rainbow Dash.

A being called Naturus has came and for an unknown reason, he killed off the crystal ponies, merponies, griffons and dragons. His invasion pattern seems pretty unusual at first. First, he hit the Crystal Empire and replaced it with his own fortress. His forces moved west and destroyed the merpony kingdom of Aquastria, then went east and killed off the griffons, and even wiped the mighty dragons themselves to extinction. From various rumors, Naturus would absorb an item and continue on with his rampage.

The only dragon left is Spike, and Naturus kidnapped him and is keeping him hostage.

I don't know what he's doing, but we need to stop him before he winds up destroying the rest of Equestria and her neighbors. Shining Armor has resumed his role of Captain ever since he completely healed, and we are now going to war with him.

--Twilight Sparkle

--A FEW HOURS LATER...

"We've heard you, but, it turns out, the Everfree is invading, AGAIN!!!" Applejack said.

"WHAT, AGAIN!!!" Twilight said.

"Well, darling, we came here as fast as we can, I don't want my horn to be on the fritz again." Rarity said.

"Naturus must have seen it coming, and has done something, quick girls, there's no time to waste!"

"Let's go! I haven't had an adventure in quite a while!" Rainbow Dash said.

"Ah also wanna go, ah was geetin' bored." Applejack said. "Yeah, I want action too!" Pinkie Pie said. "Um, the animals aren't acting like their usual selves, so I'm coming." Fluttershy said. "Then let's ride!" Twilight said as she teleported the group to Ponyville.

After the teleportation, Twilight looked around, plunder seeds were everywhere, but not this much. Clouds were storming, and unlike last time, the animals were going berserk, some of them were Fluttershy's animals. Unicorn magic was going haywire, and the sun and moon were fighting against the princesses' magic.

What's even worse was that zoo animals escaped from their cages, and even species she didn't know about were appearing in mysterious flashes of light.

Weird birds with teeth and long, bony tails (Velociraptor, Troodon, Deinonychus) were eating the ponies, if they locked the doors, apes and monkeys will sneak in and unlock the doors from the inside. If they barred their windows, stronger animals like bighorn sheep and those strange reptiles with bony heads (Pachycephalosaurs) will bash through, letting other animals inward.

Even the skies themselves were no longer safe, for not only clouds, but birds of prey, what looked like non-sentient dragons, and giant bat-reptile hybrids (Pterosaurs) were flying in the sky, ready to snatch any pegasus that dares to fly away. Twilight broke out of her stare when she heard Fluttershy talking to a bunch of those long-tailed birds.

"What the? I can't understand a WORD they're saying, I can, wait, are they hissing at me?" Fluttershy said as one of the larger birds attempted to leap at her. "EEP!!!" Fluttershy galloped around being chased around. Twilight rolled her eyes and shot a beam at one of the birds, but it saw the beam coming and dodged it at the last second.

"Gah! They don't understand Fluttershy, and one of them dodged my magic,this is unnatural! We've got to go into the forest!" Twilight said as she and her friends galloped into the forest. As they were galloping, they passed a corpse of a familiar zebra being eaten by scavengers.

When they went to the cavern, they found that the Tree was... GONE!!! Only a gaping hole where it was.

"NOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!" Twilight screamed at the top of her lungs. Rarity rolled her eyes and teleported the group back to Canterlot.

"PFFT! Those gay ponies really thought that I was two beings, that's rich!" Naturus said, his all-seeing eye fixated on them. He then turned his attention to Spike, who was still in his prison cell. "Wait, why did you say that they thought you were two separate beings?" Spike said.

"Allow me to tell you that the Tree was me all along, SUCKER! Those ponies really got on my nerves, my strength was weakend because of them! Even though I would have quite some time to regain full strength, I would absorb items anyways."

"Wait, that's... no... YOU'RE THE TREE OF HARMONY!!!" Spike said. "Yes, I monitored the world in that form, but since the ponies were gaining stronger influences, I decided that I had enough!" Naturus said. "Why?" Spike said as Naturus left the dungeon, leaving him in his cell.

"The new sentient races will be ready when I clean out this world!"