Countless decades ago in a place whose name has been lost to time, when Pokemon were yet to be tamed and what would be cities were mere villages, there was a little human child. This child was very lonely, as he had no friends and would shy away from others. Rather than talk to the other children his age, he would play alone in the forest with the little Pokemon who lived among the trees. He had grown to be great friends with the little Pokemon, naming them and sharing scraps of food he had pilfered from his lunch.
Yet, despite all of his Pokemon friends, he was still incredibly sad, as his family had fallen on hard times, and they struggled to earn money just to keep food on the table. The child felt guilty as he could not bring any more food to the Pokemon, nor could he help his family as he had no skills in labor.
One day after the child had returned home, however, one of the Rattatas in the woods had an idea to help the child feel better. She rallied the other Pokemon, and shared her plan. They would take the child to the guardian of the forest, who would help bring prosperity to the child's family. So, they consulted with the guardian, who agreed to help, but not before seeing the child.
The next morning, the child had returned as always, apologizing profusely for once again having no food to bring them. But the Pokemon did not seem phased, and many tugged at his shirt, pointing him somewhere. He understood they wanted him to follow, and so he did, going deeper into the forest than he ever had done before.
They came to a stop in front of what looked to be a great tree, with strange jagged carvings along the side. But then, startling the boy, the tree opened the "carvings" revealing them to be mouths, and opened its massive eye, staring at him with a glowing red pupil. The boy was frightened, and wanted to flee, but the other Pokemon would not let him. Yet it held no malice, and spoke to the boy in a loud yet calming tone.
"I am Trevenant," its voice boomed. "I have been told that you are a friend to the Pokemon of the forest, and were in need of my help."
The little boy nodded.
"So I shall assist you, then. Lead me to your farms, I will make the crops bountiful."
With that, they headed to the boy's home, and Trevenant stayed to its word. The plants grew faster than the boy had ever seen, the fruit trees blooming and the vegetables becoming incredibly plump. Amazed and grateful, the boy thanked Trevenant for its kindness, with the mighty tree returning to the woods. And, full of excitement, the boy told his parents of the miracle. His parents wept with joy, and quickly got to harvesting, with enough food to give them a proper meal and to sell while still having some to spare.
However, over time, the other people grew jealous of the family and their sudden luck. "Why should we go hungry while they have success?" some said. "How could they have gained so much so quickly?" others asked. Then, one angered person rose up with what he thought to be the answer.
"It's a family of witches!" he preached to the others, rallying them together out of their shared jealousy and hatred. "They've used their witchcraft on the soil, and tainted our humble village!"
Too blinded by their jealousy to call it nonsense and too blinded by their rage to check the truth, the people of the village joined together with what few weapons they had, and stormed the house of the boy's family, eager to drive them out of town. When the family looked outside to see what the commotion was, they found their house surrounded, people shouting accusations at them, threatening them with their torches. The child stayed hidden inside the house, while the parents stood their ground, unsure of why they were being accused. But they were unable to hold off the whole village, and by the time the child had peeked out the door to see if the noise had died down, all he found was his parents' bodies, their blood staining the grass.
Terrified and stricken with sorrow, the child sat down and began to cry all alone.
After a while, though, the child noticed a tall shadow now looming over him. He looked behind him to see Trevenant, who had an apologetic look in its eye.
"My gift was not meant to cause you so much harm." it told him. "While I am unsure I will be able to make up for what you have lost, I can give you something new." Then, Trevenant pointed towards the woods. "You can return to the woods and be with the Pokemon again, like before. But I am aging, and soon I will not be around to guard the woods. I can pass down my title as the guardian to you, but it comes with a warning. You might never be able to return to this place… at least, not as you are now. But it is your choice, and I understand if you cannot forgive me for my mistake."
But the boy nodded, and accepted the deal. And with that, the mighty Pokemon and the lonely human boy walked deep into the forest, neither to ever be seen by humans again.
They say, though, a Phantump had haunted the forest since that day, attacking all people from the village who dared to enter it.
Because even when the living had forgotten the injustice they caused,
the child had not.
("According to old tales, these Pokémon are stumps possessed by the spirits of children who died while lost in the forest." - Pokedex entry for Phantump from Pokemon Y)