As revealed at the end of the Emerald chapter, Emerald was one of the orphans that Crystal was helping. He looked up to her and wanted a Pokédex of his own. Professor Oak did want to offer one to him at one point but he had declined due to his animosity towards Pokémon while in the Pokémon Academy. He spent his time roaming around Hoenn and met the Trick Master, who gave him the gadgets that were inspired by a faraway land. He also had a green gem that was used as a test to call out Rayquaza, but Emerald found the gem and it got attached to his forehead. He later received the Pokédex from Professor Birch on May 31, his birthday.
Emerald without his clothes covering him
Emerald makes his first appearance when he arrives at the currently opening Battle Frontier, having been brought there by his two friends, Latios and Latias. He meets a news reporter, and saves him from a wild Sudowoodo that the reporter had accidentally angered. He quickly runs off to go and challenge the Battle Frontier and gets into a brief tussle with one of the Frontier Brains, Tucker, and crashes the opening ceremony. After being captured by the angry Frontier Brains, Emerald reveals to them about his wanting to conquer the Battle Frontier. Initially, they refuse his challenge and decide to ban him from the Frontier until a news story reveals that the reporters thought that the Frontier Brains allowed Emerald to take part in the Battle Frontier. With the risk of losing major publicity, the Frontier Brains and Scott eventually agreed to his challenge: he would defeat all of the seven Brains within seven days.
Noland decides that he will be the first to challenge Emerald and the next day, Emerald begins his Battle Factory challenge. He manages to win 40 consecutive battles, allowing him to challenge Noland, the Factory Head. Despite having a team of random Pokémon, Emerald eventually manages to come out on top and wins the Knowledge Symbol. Later that night, Emerald reveals to the reporter that he had taken the Sceptile he used to beat Noland, revealing that it is in fact, not a rental Pokémon.
Tucker and Brandon arrive to try to get Emerald to challenge their facilities next but end up getting into a fight that gets them stuck to one of the Battle Pike's fangs. The day after, Lucy finds, and frees the three from the Battle Pike's fang while telling Emerald to challenge her facility next. After getting three new Pokémon from his source, Emerald goes through the Battle Pike and its various traps ranging from wild Pokémon battles, to Status ailment inflicting Pokémon, to rooms that don't have any danger at all. Emerald manages to go through all 139 trap-filled rooms and reaches the Frontier Brain, Pike Queen Lucy. The two battle each other; despite Lucy's strategy to poison Emerald's Pokémon, she is eventually defeated by his quick thinking. Emerald wins his second Frontier Symbol and goes to calm down the Pokémon he encountered in the Battle Pike, revealing that they, like his Sceptile, aren't actually Rental Pokémon and were planted there by someone.
Emerald and the reporter are approached by Brandon who tells Emerald to challenge his facility next and throws him in the Battle Pyramid. Emerald picks a new set of Pokémon to use for his challenge and goes inside of the dark maze. He eventually manages to the peak of the Pyramid and begins his battle with Brandon and his legendary Regirock, Regice, and Registeel. Despite Brandon's powerful Pokémon, Emerald manages to defeat all of them and wins the Brave Symbol.
Just as Emerald leaves the Battle Pyramid he is ambushed by Anabel and the other Frontier Brains. The Brains believe that Emerald was the one who had stolen the Battle Factory's Rental Pokémon and attacked Noland. Emerald tries to prove his innocence by revealing why he came to the Battle Frontier, to capture the legendary wish granting Pokémon, Jirachi. Emerald, the Frontier Brains, and the reporter all travel to the Artisan Cave where Jirachi is rumored to be resting. Emerald easily escapes the wild Smeargle that live in the cave and eventually finds Jirachi resting at the center of the cave. Just when he tries to capture Jirachi, Emerald is attacked by the armored Guile Hideout. Emerald and Anabel battle the mysterious villain while trying to capture Jirachi; in the end, Guile manages to stop them while Jirachi escapes.
The injured Emerald, Frontier Brains, and the reporter all return to the Battle Frontier where Emerald starts his Battle Arena challenge. Emerald easily makes it through the Battle Arena and battles Greta in the final match and comes out the victor after doing something he’s never done before, cheering on his Pokémon, and wins Guts Symbol in the process. After he defeats Greta, Emerald and his Pokémon fall asleep and are taken into a hotel room by Greta and the reporter. When Greta and the reporter notice that Emerald’s clothes would be uncomfortable to sleep in, they decide to take them off and put him in a pair of pajamas. After they strip him down to his underwear, they are shocked to find out that Emerald is unusually short. The reporter tells Greta to ignore this and sends her out of the room while Emerald’s Pokémon get into a fight over who gets to care for him while he sleeps.
The next day, Emerald decides to go to the Battle Dome as his next challenge and battles the many Trainers that have come to the Battle Frontier to take part in it. After taking a bathroom break, he meets Ruby and Sapphire, two other Pokédex holders from Hoenn. They reveal that they have come to help Emerald on his quest to find Jirachi but Emerald states that he doesn’t need help and attacks them. Later, at the Battle Dome, Emerald, Ruby, Sapphire, and Tucker all make it to the semi-finals of the tournament.
The first round of the semi-finals is Emerald facing off against Ruby, with the second being Tucker versus Sapphire. Ruby and Emerald battle each other and Ruby constantly annoys Emerald to the point of nausea by talking about the bonds he has with his Pokémon. Just when it seems like Ruby is going to win, Sceptile manages to finish off Ruby's Feefee, making Emerald the winner. The final match is Emerald versus Tucker (who had defeated Sapphire) but Emerald reveals that he wants to switch his team for a different one. Tucker gives him permission to do so and Emerald changes his team, stating that if he makes bonds with his Pokémon, then he is just insulting them. Emerald returns with a new set of Pokémon and battles against Tucker but is easily defeated by him.
A depressed Emerald walks out of the Battle Dome and immediately leaves to the Battle Palace, where he challenges Spenser for a match. Spenser explains that Emerald needs to pick three Pokémon he trusts the most and that they will battle without his commands. Emerald chooses Sceptile, Sudowoodo, and Dusclops, who he still has doubts about trusting. Just before they can even start the match, Spenser's phone rings with a message that reveals that Guile Hideout has captured Jirachi and is attacking the Battle Frontier with Rental Pokémon. Emerald decides to trust his Pokémon and leaves to the Battle Tower along with Ruby and Sapphire to defeat Guile once and for all.
Emerald in the sixth chapter
The three meet up with Noland and go through the Battle Tower where they find Anabel, mind controlled by Guile Hideout. Emerald eventually makes it to the top of the Battle Tower where he faces Anabel and loses to her powerful Raikou. However, Latios arrives in the nick of time to return Emerald's Pokémon to him, along with the Spirits Symbol they won at the Battle Palace. Anabel collapses from not being able to handle the mind control and Latios and Latias use their power to reveal Guile Hideout’s true identity.
Guile manages to make his wish; a giant sea monster is created from the water surrounding the Battle Frontier and attacks the island. The Battle Tower's "Disaster Prevention System" activates and the Hoenn Pokédex holders begin fleeing. Emerald accidentally gets stuck in one of the doors and is surprisingly rescued by Guile Hideout; however, this Guile is quickly revealed to actually be Gold in disguise. Gold reveals that he and Crystal had come to help defeat Guile and free the Pokédex holders that were petrified at the end of the FireRed & LeafGreen chapter.
Gold gives Emerald the task of asking Jirachi for a wish to reverse the petrification of their senior Pokédex holders. Emerald attempts to get Jirachi to grant his wish but to no avail and becomes disheartened. Dejected, Emerald goes to train with Ruby and Sapphire to help his Sceptile learn the ultimate move, Frenzy Plant but is too depressed to focus. Emerald reveals his past to Ruby and Sapphire about how he obtained a Pokédex, got his mechanical suit, and how he got the mission to go to the Battle Frontier. Just as he finishes his story, their Pokémon finish learning the ultimate moves while Gold and Crystal fall on top of their training room, completely defeated by Guile.
Angered that Guile had hurt Crystal, Emerald attacks Guile but is easily sent flying by his sword. Guile taunts Emerald by stepping on his Pokémon; Emerald tries to get him to stop but Guile reminds him about his "liking Pokémon battles instead of the Pokémon themselves" philosophy. After hearing Guile insult his Pokémon and friends, Emerald angrily shouts that he truly does love Pokémon and the people who love them. His words cause Jirachi’s third eye to open and grant his wish to revive the petrified Pokédex holders. With their seniors revived, they join the fight against Guile and his army of Rental Pokémon. As they battle, Emerald comes up with a plan to defeat the giant Kyogre while Gold and Red manage to outsmart Guile and destroy his armor. After the plan is fully set up and Emerald successfully calming down the rampaging Rental Pokémon, the ten Pokédex holders have their Pokémon fire off the ultimate moves, Hydro Cannon, Blast Burn, Frenzy Plant, and Volt Tackle to finish off the giant sea beast, once and for all.
With the monster Kyogre finally defeated, Emerald fishes Guile out of the water and forces him to reveal where he got the armor. After explaining, Guile finds his armor floating in the water and breaks free of Emerald’s grip to try to get it back but only finds that it was the fake armor Gold had worn earlier. Guile then disappears in a bright flash of light, armor and all while Emerald falls asleep from exhaustion; Latios and Latias, finally happy that Emerald has found friends, say their goodbyes and leave to Southern Island.
Later that day, Emerald wakes up from his nap and finds that his Pokémon have bonded with the other Pokédex holder’s Pokémon. The Frontier Brains come and thank Emerald for his help and he is given the Ability Symbol by Anabel. Emerald and the reporter quickly remember that there is only day left for his final challenge and they ask Tucker if he can schedule at tournament. Tucker explains that even though the Battle Dome was undamaged in the fight, there aren’t any people to hold a tournament; Red then comes up with the idea to host a Pokédex holder tournament, an idea Scott happily agrees to. Emerald is seen saying his goodbyes to Jirachi as it returns to its thousand year slumber once again. Emerald goes to battle in the tournament where it is shown that he managed to win the Tactics Symbol.
Emerald with his hair down
Emerald appears as a cameo when Crystal talks to Silver about how she wants to protect the world so that children will be able to chase their dreams.
In the thirteenth chapter, Emerald, along with Ruby and Sapphire, is enlisted by Steven to learn Mega Evolution in order to prevent a disaster that will strike Hoenn. He and Sapphire train with Ultima at Dewford Town on the ultimate moves in order to prepare them for their Mega Evolutions. Whilst on a break, Sapphire complains that Ruby has not yet arrived to train with them. Emerald quells Sapphire's worries by pointing out that Ruby invited her to see the Litleonid meteor shower after their training had finished. Later, Emerald and Sapphire manage to successfully Mega Evolve Sceptile and Chic into Mega Sceptile and Mega Blaziken. Unable to wait for Ruby to return, Mr. Stone decides to use the energy produced from the Mega Evolution to power a machine to prevent the disaster.
The group travels to Sea Mauville, where the machine that will drain their Pokémon's energy is located. While Steven and Mr. Stone prepare the machine, Emerald explores the area with Sapphire. Later that night, Emerald is attacked by a mysterious Pokémon. Angered, Emerald chases after the Pokémon, only for it to dodge his attacks. Even when Steven steps in with his Mega Metagross they are unable to stop the Pokémon before it eventually escapes.
The next day, Steven and Mr. Stone begin to use the Absorber to drain Emerald's Sceptile and Chic in their Mega-Evolved states. The process hurts their Pokémon intensely, causing their Trainers to be horrified. After the process is finished, they are attacked by Zinnia, a Draconid with a hatred for the Devon Corporation. She attacks with her small army of former Teams Magma and Aqua Grunts to destroy the dimensional shifter that was powered by Sceptile and Chic's energy. Sapphire takes the shifter and tries to keep it away, but the Pokémon that attacked Emerald earlier transported her to somewhere else with its hoops. When Ruby arrives to stop the fighting, Emerald informs him that the Pokémon, Hoopa, is the cause of Sapphire's disappearance. Ruby convinces Zinnia to leave by offering up his and Emerald's Mega Bracelets as a bribe.
The group continues traveling to learn more about Rayquaza, which is a key in stopping the meteoroid. During the trip, Emerald reunites with Latios and Latias, who tell them about Hoopa and the Diancie Ruby befriended before he arrived. They are attacked by Blaise and Amber so that they can use Hoopa's power for their own plans. With the power of Blaise's illusions, the two manage to manipulate Hoopa into summoning Groudon and Kyogre from its hoops. Groudon and Kyogre immediately begin heading towards somewhere and easily shrug off Ruby and Emerald's attempt to stop them. Ruby and Emerald discover the culprits and attempt to stop them, only for both to escape and trap Emerald and Ruby in an illusion.
After escaping the illusion, Emerald and Ruby find that Groudon and Kyogre have transformed into new, more powerful forms. Emerald attempts to fight, but Ruby states that getting to Meteor Falls is more important. Despite this, Emerald and Ruby are unable to get past the power that Groudon and Kyogre are now exerting in their Primal forms. They soon find out that the ones responsible for Groudon and Kyogre's Primal Reversion are Maxie and Archie, who are still alive. Maxie and Archie use the power of the super-ancient Pokémon to easily overpower Emerald and Ruby, defeating them and knocking them out of the sky. Maxie and Archie gloat over their victory and reveal that their return is all for the sake of saving the planet from the meteoroid threatening to destroy it.
Emerald and Ruby awaken at the Meteor Village, a small town hidden inside of Meteor Falls and home of the Draconids. There, they find that only four days remain until the meteoroid hits. The village Elder reveals that Sapphire battled Zinnia in order to protect the dimensional shifter but was defeated and went missing. The Elder also states that she gave gave Archie and Maxie a place to train in preparation to destroy the meteoroid. Despite this, Ruby decides to continue with trying to find Rayquaza, as he believes he may have its trust after battling with it four years ago. After meeting with his father again, Ruby and Norman use Hoopa's rings to transport them to the Pokémon Association's research facility in Goldenrod City, where Rayquaza was seen heading towards.
After Ruby and Norman find Rayquaza, Emerald uses Hoopa's rings to search for Sapphire. They manage to track Sapphire to Route 120, where she ended up landing after her defeat by Zinnia. Just as they manage to see Sapphire, Archie and Maxie appear, having finished their training. When it sees Kyogre and Groudon through the ring, Rayquaza goes berserk and rushes towards the ring to confront the two. In order to prevent a battle from going on, Hoopa directs the ring connecting Goldenrod to the Meteor Village to the other ring, causing Rayquaza and Ruby to appear in Route 120.
Maxie and Archie chase after Rayquaza by forcing their way through Hoopa's ring. Unable to handle the stress of both Groudon and Kyogre moving through its ring at the same time, Hoopa is injured and collapses. Emerald then leaves the village and heads to Route 120 with Latias and Latios.
Later, Emerald meets up with Ruby and Sapphire after Zinnia managed to lure Rayquaza away from them in an attempt to get it to join her. He reveals that Zinnia's planned failed, and ended with Rayquaza violently lashing out at Zinnia and blasting her into the ocean. They head down to Sootopolis City, where Zinnia was taken to after being rescued by Latios. There, they meet with Steven and Mr. Stone again. Mr. Stone attempts to apologize to Zinnia for the trouble he caused in attempting to control Rayquaza. Zinnia rejects Mr. Stone's apology and claims that he is only trying to save face for his failures. Now brought to tears, Zinnia gives up and claims that her villagers were right to believe she wasn't strong enough to save the planet in place of Aster, the previous Lorekeeper. Zinnia and Mr. Stone's behavior angers Emerald, who claims that they shouldn't give up and there must still be something they can do to save the planet.
Emerald suggests that the three plans to stop the meteoroid should stop fighting one another and instead work together. The group is approached by Giovanni, Red, Green, Blaise, and Amber, who all reveal that despite not being in battle, Mega Evolution is still able to be activated, which suggests that the meteoroid may be a Pokémon from space. Later, the group has various allies from around Hoenn travel to Sootopolis to lend their assistance in stopping the meteoroid.