The Emperor apparently came from kingdom beyond the farthest shores of Never. The Emperor was apparently ignored by other powers and kingdoms, this was what he apparently used to his advantage. While they ignored him, this helped his strength grow more in power with each battle and conquest. Many Fables have not really seen him, rumors had it he was a woodland sprite and some say he was a god; who had been thrown from the Heavens when his corruptions became too great for his lofty brethren to tolerate. In Fables Legends In Exile, some of the Fables believed him to be a type of satyr or Lucifer looking monster.
However, this was all most likely fabricated to glamorize or make him appear more terrify to his enemies. Unknown to all, but perhaps Lumi, was that the Emperor was really no more than a very well made puppet by Geppetto. He used the Emperor to serve as the mastermind, when in reality it was Geppetto pulling the strings all along. The Emperor was brought to life using an elixir from the Blue Fairy, whom Geppetto had knocked unconscious. Due to Pinocchio's constant adventures, leaving Geppetto alone, the Blue Fairy had now put loyalty spells on any of Geppetto's future children, including the Emperor. This is a secret, Geppetto and the Snow Queen have gone to great lengths to hide from his enemies and allies.
During his raise to power, the Emerald Kingdom in Oz was one of the many kingdoms he conquered. One by one, he defeated many including the Great Lion, though many of the Fables when they were in the Homelands did nothing. This would be a mistake as he eventually began to conquer the Homelands spreading like a plague, most likely with the help of Geppetto's wooden soldiers and goblins. Due to this, this caused the Fables to flee and leave the Homelands for mundane world.
However this didn't hide them from the Emperor, as Bigby and the others often kept eyes out for spies. Using Cinderella, they discovered one of their own, Ichabod Crane had planned to betray Fabletown and join the Emperor. However, he was stopped. In Homelands arc, Boy Blue foolishly attempted to kill the Emperor using the vorpal sword and his magic cape. While he managed to get in and beheaded the Emperor, it was too good to be true. The Ice Queen froze him before he escaped.
Blue awoke in a cage and much to his surprise, Geppetto was there along with the Emperor's head. And it is there, he discovers the truth about the Emperor and what Geppetto really is. As the day went Geppetto explained how he himself became the real Adversary. Through promises of seeing Red Riding Hood, Blue gave Geppetto the now apparently dead wooden Pinocchio. Geppetto revived him with the elixir, this didn't stop Boy Blue's determination to leave. He escaped with Red, but had to leave Pinocchio due to his loyalty spell. Pinocchio was now part of his "brother's" kingdom.
While not much has been shown with either relationship, Pinocchio seemed to go about with his new life. Mostly getting drunk, and often seen wandering away from home. During the Emperor's birthday, Pinocchio tried to be kind and give his father a birthday present. While his relationship with Lumi has never been fully defined, he is often seen consulting with her and was shown most distressed when she was under the affect of Briar Rose's sleeping curse.
Unlike the wooden soldiers, the Emperor is shown to have more intellect and is shown to express different opinions. But due to the spell, he's often forced to obey and listen to his father's word. Eventually in War and Pieces arc, the Emperor was defeated by Bigby Wolf and the assistance of Prince Charming who sacrificed his life.
However, his story may not be over yet.