After running away from his relatives, Emerald created a new look to reinvent his image. This got the attention of the inventor, the Trick Master, who suggested Emerald move to Earl Dervish's Pokémon Academy, an orphanage. After arriving, Emerald encountered Crystal, a kind caretaker at the orphanage that was skilled at catching Pokémon. Wanting to learn from Crystal, Emerald met with Professor Oak to obtain a Pokédex like she did, but was refused due to his dislike of Pokémon. Oak allowed Emerald to temporarily register himself as a Pokédex's owner and told the boy to go out and find something unique about himself. With gadgets created by the Trick Master, Emerald changed his looks and honed his ability to determine a Pokémon's birthplace. Later, he received his Pokédex on his eleventh birthday.
Emerald debuted in Never Spritz a Knotty Sudowoodo, where he arrived at the Battle Frontier and rescued Todd, a reporter, from a wild Sudowoodo he angered. Afterward, Emerald crashed the opening ceremony press conference and announced his plan to conquer the Battle Frontier. While they initially refused Emerald's challenge and almost had him banned, the Frontier Brains decided to allow Emerald to participate when the press mistook his intrusion for a publicity stunt. As the Frontier would not open for another seven days, Emerald had until then to complete all seven facilities.
Emerald in the sixth chapter
The next day, in Interesting Interactions Involving Illumise, Emerald challenged the Battle Factory. Despite having a team of random Pokémon, Emerald eventually managed to defeat the Factor Head, Noland, and obtain the Knowledge Symbol. Later that night, Emerald revealed to Todd that he took the Sceptile he used to defeat Noland. With Latios and Latias' assistance, Emerald deduced that Sceptile was not a rental Pokémon and had been planted in the Battle Factory by someone other than Noland.
In As Luck Would Have It, Kirlia, Emerald challenged the Battle Pike. As the facility had no rental Pokémon, Emerald instead used a party of Pokémon received from Crystal. After making his way through the various traps located in the Battle Pike, Emerald faced off against Lucy, the Pike Queen, and won, earnin the Luck Symbol. Afterward, he, Todd, and Latias searched through the rooms of the Battle Pike to calm down suspicious Pokémon that were also planted like Sceptile.
In A Dust-Up With Dusclops, Emerald challenged the Battle Pyramid with another set of Pokémon received from Crystal, Emerald traversed through the Pyramid's dark maze. After making his way to the peak, Emerald faced off against the Pyramid King, Brandon and his powerful Pokémon Regirock, Regice, and Registeel. Eventually, with Sceptile's assistance, Emerald managed to defeat Brandon and earn the Brave Symbol.
In A Sketchy Smattering of Smeargle, Anabel, the Salon Maiden, and the other Frontier Brains accused Emerald of stealing the Battle Factory's rental Pokémon and attacking Noland. To prove his innocence, Emerald revealed he came to the Battle Frontier to capture the Wish Pokémon, Jirachi. Emerald, the Brains, and Todd all traveled to to the Artisan Cave, where Jirachi was rumored to be resting. Emerald managed to find Jirachi at the center of the cave, but his attempt to capture it was impeded by a man wearing armor known as Guile Hideout, allowing Jirachi to escape. Angered that he lost his chance at Jirachi, Guile fled as well, launching an attack from his sword to hide his escape. Sceptile, the Sudowoodo that attacked Todd, and a Dusclops from the Battle Pike appeared to protect Emerald from the attack.
In Sneaky Like Shedinja, Emerald challenged the Battle Arena. Instead of another party of Pokémon from Crystal, Emerald instead used Sceptile, Sudowoodo, and Dusclops. During his battle against Greta, the Arena Tycoon, Emerald managed to win by cheering his Pokémon on, something he wouldn't do normally. After winning and obtaining the Guts Symbol, Emerald and his Pokémon passed out from exhaustion and are taken to a hotel room by Greta and Todd. Assuming his regular clothing would be uncomfortable to sleep in, Todd and Greta try to change Emerald into a pair of pajamas, only to discover that the boy is unusually short, much more so than they had expected. Todd had Greta pretend she didn't see anything and sent her out of the room.
In Verily Vanquishing Vileplume I, Emerald challenged the Battle Dome. While on a bathroom break, Emerald met Ruby and Sapphire, the two other Hoenn Pokédex holders. When they revealed they were sent to assist with the Jirachi capture mission, Emerald rejected their help and ran off. Ruby and Sapphire also entered in the Dome tournament, eventually making it to the semi-finals alongside Emerald and Tucker, the Dome Ace. Emerald faced off against Ruby and won while Tucker defeated Sapphire, allowing both to face each other in the finals. Finding Ruby and Sapphire's constant talk about bonding with Pokémon annoying, Emerald had them kicked out of the Dome and decided to switch his party out, stating that he'd be insulting his Pokémon if he bonded with them. After receiving his new Pokémon, Emerald battled against Tucker, but was easily defeated.
In Standing in the Way with Starmie, a depressed Emerald left to go challenge the Battle Palace, where he went up against Spenser, the Palace Maven. Spenser explained that in order to battle against him, Emerald must use three trusted Pokémon and have them fight without his commands. Before their battle could begin, Spenser received a call from his fellow Brains revealing that Guile managed to capture Jirachi and has sent an army of rental Pokémon to attack the public. Putting his trust in Sceptile, Sudowoodo, and Dusclops, Emerald left them behind and went with Ruby, Sapphire, and Noland to confront Guile at the Battle Tower. Along the way, Emerald calmed down a rampaging Mr. Mime, Snorlax, Mantine, and Mawile. In order to battle, Noland decided to use Mawile while allowing Emerald to keep the other three.
Emerald without his clothes covering him
In Facing Gulpin Is Hard to Swallow, Guile forced the Hoenn Pokédex holders and Noland to take the Battle Tower challenge in order to make it to him. After battling through various virtual Trainers, Emerald finally made it to the final floor, where he faced off against Anabel, who had been put under Guile's mind control. After Emerald was defeated, Latios appeared and returned Emerald's other three Pokémon, who had successfully obtained the Spirit Symbol. Using his Sight Sharing, Latios relayed a message from Spenser, who revealed that he came in contact with the Blue Orb in the past and gained the ability to detect others like him, which included Guile. With his identity exposed, Guile lifted his helmet, revealing himself to be Archie, the leader of Team Aqua.
In The Final Battle I, Guile used Jirachi's wishing granting power to summon a giant Kyogre-shaped mass of seawater and had it flood the Battle Frontier. Emerald and the others were assisted by Crystal alongside Gold, another Johto Pokédex holder. The two revealed that their fellow Pokédex holders were turned to stone and the only way of reviving them was Jirachi. While Crystal and Gold kept the Kyogre monster busy, Emerald was tasked with making the wish to revive the petrified Pokédex holders, but Jirachi refused his wish and flew away. Afterward, the Hoenn Pokédex holders trained to learn the Ultimate Moves, Frenzy Plant, Hydro Cannon, and Blast Burn.
In The Final Battle III, Emerald struggled to focus with the training. At Ruby and Sapphire's suggestion, Emerald revealed his past and how he obtained a Pokédex, got his mechanical suit, and got the mission to go to the Battle Frontier. Once he finished, Gold and Crystal fell on top of the training room, having been defeated by Guile. Angered that he hurt Crystal, Emerald tried to attack Guile, but was defeated. When Guile reminded Emerald of his earlier statements of only liking, Emerald angrily admitted that he truly does love Pokémon as well as the people who love them. His words caused Jirachi’s third eye to open and grant his wish to revive the petrified Pokédex holders. In The Final Battle VII, the ten Pokédex holders gathered together for one final battle against Guile and his army of rental Pokémon. With the help of Scott, Todd, Latios, and Latias, Emerald created a giant field around the Battle Frontier that pacified all of Guile's rental Pokémon with soil from Faraway Island. By utilizing a triple Frenzy Plant, Hydro Cannon, Blast Burn, and Volt Tackle combination, the Kyogre sea monster was overloaded with energy and exploded, finally ending the conflict with Guile.
In Epilogue, Emerald was congratulated by his allies on his victory against Guile. After receiving the Ability Symbol, Emerald realized there was only one day left to obtain the final Symbol and begged Tucker to let him challenge the Battle Dome again. Tucker allowed Emerald to compete, but without any other Trainers to join in the tournament, Emerald had to go up against his fellow Pokédex holders instead. As Jirachi went back to its thousand year slumber, Emerald thanked it for granting his wish to have friends. Afterward, Emerald competed in the Pokédex holder tournament, which he ended up winning, earning him the Tactics Symbol.
In High-tailing It from Haunter, Emerald was briefly seen together with the other Pokédex holders from Kanto, Johto, and Hoenn when the Advanced level Grunt was talking to Diamond about the Pokédex.
In the thirteenth chapter, the Hoenn Pokédex holders were enlisted by Steven and Mr. Stone to prevent a meteoroid from crashing into the Earth and destroying it. Steven gave the three a Mega Bracelet, enabling them to use Mega Evolution and had them train with Ultima so Sceptile, Mumu, and Chic could fully master the Ultimate Moves. Ruby only agreed to help on the condition that Sapphire be kept in the dark about the meteoroid.
In Omega Alpha Adventure 0, Emerald watched Sapphire train her new Kirlia, Kirly, and Ruby's Rara in order to evolve them into a Gardevoir fighting pair, only for Sapphire to accidentally kick up a Shiny Stone, causing Kirly to evolve into a Gallade instead. Later, Emerald and Sapphire fully mastered the Ultimate Moves with Ultima's guidance and gained the ability to use Mega Evolution. In order to prevent potential enemies from finding them, Mr. Stone had the training moved to the abandoned energy harvesting facility, Sea Mauville.
In Omega Alpha Adventure 5, the group arrived at Sea Mauville. That night, Emerald encountered the mysterious Pokémon, Hoopa, which couldn't be pacified by the soil from Faraway Island. Even with assistance from Steven and his Mega Metagross, Hoopa managed to escape. The next day, Emerald and Sapphire assisted Steven and Mr. Stone by putting Sceptile and Chic on a machine known as an Absorber and using the power of the Ultimate Moves in their Mega-Evolved forms. To their horror, the machine drained both Pokémon of their life energy to fuel a special device known as the dimensional shifter.
In Omega Alpha Adventure 8, the Draconid Zinnia and a group of Team Aqua and Magma Grunts attacked the Sea Mauville in order to destroy the dimensional shifter. During the clash, Zinnia stole Sapphire's Mega Bracelet, and Sapphire ended up falling into one of Hoopa's rings. Sapphire was transported to the inside of a rocket located at Mossdeep City, where she handed the dimensional shifter to Professor Cozmo and his assistants. Later, Ruby arrived to assist in the battle against Zinnia. When Zinnia tried to take Steven's Key Stone as well, Ruby offered up his and Emerald's Mega Bracelets as a bribe. Zinnia accepted and left, completely unaware that Ruby managed to steal a special scroll from her when she wasn't looking.
In Omega Alpha Adventure 10, the group traveled to Meteor Falls in hopes of finding information about Rayquaza. Hoopa was attacked by Amber and Blaise and manipulated into summoning Kyogre and Groudon with its rings. Using an illusion, Blaise and Amber bought themselves enough time to escape and allow Kyogre and Groudon to revert to their Primal forms. To Emerald and Ruby's shock, Archie and Maxie had returned and were the ones who gave Kyogre and Groudon the Orbs necessary for Primal Reversion. Using the super-ancient Pokémon's power, Archie and Maxie easily knocked Emerald and Ruby out of the sky before revealing that they also intended on stopping the meteoroid.
In Omega Alpha Adventure 14, Emerald and Ruby awakened at the Meteor Village, the home of the Draconids. The village Elder revealed that Sapphire fought to protect the dimensional shifter, but lost and went missing. The Elder also allowed Archie and Maxie to train and teach Kyogre and Groudon moves necessary for stopping the meteoroid. After meeting with his father again, Ruby and Norman determined that Rayquaza must be heading towards the Pokémon Association's research facility in Goldenrod City and used Hoopa's ring to head there as well.
In Omega Alpha Adventure 16, Emerald used Hoopa's rings to search for Sapphire, eventually managing to find her in a Secret Base at Route 120. Once Ruby and Norman succeeded their mission, they had Emerald tell Hoopa to create a space back to Hoenn. When Archie and Maxie emerged after finishing their training, Rayquaza went berserk upon spotting Kyogre and Groudon and began attacking them. Panicking, Hoopa moved the ring connecting to Johto to the direction of the other one connecting to Sapphire's location, accidentally sending Ruby and Rayquaza to Route 120 in the process.
In Omega Alpha Adventure 17, Archie and Maxie emerged at Route 120 after having Kyogre and Groudon force their way through Hoopa's ring, causing it to pass out. Emerald traveled to Ruby and Sapphire's location, where he revealed that Zinnia tried convince Rayquaza to join her, but was rejected and attacked. Latios rescued Zinnia and took her to Sootopolis City to recover from her injuries. Brought to tears, Zinnia gave up and admitted there was no way to save the planet anymore. Emerald disagreed and suggested the three factions that tried to stop the meteoroid work together instead of fighting with each other.
In Omega Alpha Adventure 20, the group's allies from around Hoenn gathered together to lend a hand and stop the meteoroid, now known as Grand Meteor Delta. Ruby and Sapphire set off with Rayquaza to space, and with the power of Mega Rayquaza and the combined might of their allies from Hoenn, Kanto, and Johto, Emerald, Ruby, and Sapphire successfully shattered Grand Meteor Delta into pieces. A Deoxys emerged from the wreckage of the meteoroid, but was defeated when Rayquaza shattered its core, knocked it unconscious. Afterward, Rayquaza took Ruby and Sapphire back down to Earth, where they reunited with Emerald and the others.
With the crisis averted, Emerald celebrated not having to worry about the world ending. Afterward, Emerald said his farewells to Ruby and went to meet with the Frontier Brains.