The Tree of Beginning is an anime exclusive location that first appeared in Lucario and the Mystery of Mew. Mew's supposed "home". Although an anime exclusive, it is canon in the Pokémon universe. It is known as the tree that created all Pokémon that dwell on the earth, including the Legendaries. It's unknown if Mew or the tree came first, and it seems that will always remain a mystery.
Although it looks like a tree, it is actually a rock formation. At the start of the movie, there was a battle between a green side and a red side. Aaron goes to the Tree of Beginning to meet with Mew so that he could give Mew his own aura to stop the fighting. Once his aura went to Mew, Mew directed it to the tree of beginning. The tree of beginning connects all the crystals in the land, and once the aura was transferred to the tree, all the crystals glowed green, and the battle stopped. However, Aaron's life was sacrificed.
Long after that, Ash and his friends arrive at Cameran Palace. Later into the movie, Mew takes Ash's Pikachu and Team Rocket's Meowth to the Tree of Beginning. Ash, his friends, Lucario, and Team Rocket go looking for them at the tree of beginning. Once there, they find that the tree is actually alive even though the tree is a rock formation. They also find that there are white blood cells shaped like Pokémon that eat anything that are considered threats to the tree and that Regirock, Regice, and Registeel also protect the tree from threats as it's guardians. Ash finds Pikachu, but the tree's white blood cells attack him and his friends. He then tells Pikachu that he loves him, and then the tree's white bloods cells eat and kill him and his friends. Mew then tells the tree that Ash is a friend so that Ash and his friends are resurrected, but then the ecosystem began to start breaking down due the transfer of energy being disrupted with the system's immune response being too strong which lead to an out of balance causing the tree to go into shock, causing Mew to become sick. The green crystals begin turning red because of Mew's sickness, and the crystals. Luckily however, Lucario sacrificed himself to make the tree healthy again.
Mew and the tree are connected as one. Together, Mew and the Tree of Beginning created all Pokémon including Legendaries and the Sinnoh region Legendaries Arceus, Dialga, Palkia, and Giratina. No Pokémon except Mew is as powerful as the tree of beginning and the only life form the tree cannot eat or kill is Mew. Mew and the tree have vast knowledge of the entire world. The tree and Mew work together to create peace and prosperity for the Pokémon world and all who dwell on it.