Emerald begins explaining his past to Ruby and Sapphire. When he was younger, Emerald's parents died, making him an orphan. Emerald was passed around his various relatives, but their children would just make fun of his small size. The Pokémon there would accept Emerald regardless of his size, and would help him perform various tasks that he could not perform himself due to his short stature. One day, the other children insinuated that he was just using the Pokémon as tools to make up for his short size. This angered Emerald, who tried to fight his relatives, only to beaten up. He then decided to distance himself from Pokémon so no one would ever have the same impressions of him again, and ran away.
At one point, Emerald overheard a couple of scientists arguing as he passed by a river. The male scientist wonders if it's really alright to just abandon the project to create the Green Orb, but the female scientist, Professor Yanase, calmly states that it must be a sign that Rayquaza can't be controlled like Groudon and Kyogre. Emerald soon discovered the core of the Green Orb, which Professor Yanase had discarded into the river. The core inspired Emerald to change his image into one that makes him look more independent.
Using a stick to draw in the dirt, Emerald begins designing a new image for himself. To make his legs longer, he will wear platform shoes that can turn into a water ski-like form. To make his arms longer, he will wear fake hands attached to a spring that will increase his reach. To make himself look slightly bigger, he'll comb up his hair higher and grow out his eyebrows. Lastly, Emerald decides to wear the Green Orb core on his forehead. Suddenly, the Trick Master appears, having gained an interest in the design Emerald created. Despite Emerald's loner attitude, he quickly became friends with the strange man. As they traveled throughout Hoenn, Emerald revealed that because he was passed from relative to relative, he gained the ability to identify where a Pokémon was born.
After learning about Emerald's troubles, the Trick Master decided to put him in Earl's Pokémon Academy in Johto. Upon arriving, Emerald was disappointed to see how run-down the place was. Despite how terrible the condition the place was, Emerald noticed how the helper still loved the place. Suddenly, the place is attacked by wild Slugma, but the helper quickly defeats and captures them. He later learned that the helper was none other than Crystal, and he quickly came to admire her. Emerald joined the Academy so that he could learn more about Crystal, only to find out that she had already left.
Much to his shock, various people began coming to the Academy to renovate and resupply it in order to support the orphaned children and Pokémon. Earl reveals that the person who paid for these repairs was none other than Crystal, who had become Professor Oak's assistant after leaving. Seeing how much she did for them, the children are moved to tears. Emerald, however, was stunned at Crystal's selflessness, which turned his admiration into respect.
Emerald decided that he wanted to learn from Crystal, but worried that she wouldn't have time for him because of her job. To get close to her, Emerald decided to get a Pokédex that all of Professor Oak's assistants seemed to get. After following the man to Goldenrod City, he asks Hirō to tell Professor Oak that he wants a Pokédex. As he pulls out a Pokédex, Professor Oak asks Emerald for his name.