One thousand years prior to the start of the Emerald arc, Jirachi went into a deep sleep after granting three wishes to people. Professor Oak studied a report with detailed information about the Wish Pokémon and deciphered when and where Jirachi would wake up. Professor Oak calls Scott to tell him that the place where he would build the Battle Frontier is where Jirachi would awaken next. Professor Oak sends Emerald to capture the Wish Pokémon. As of Just My Luck...Shuckle, Jirachi was set to wake up for seven days and started falling to the planet like a shooting star.
Jirachi first appeared in You Need to Chill Out, Regice, appearing above the Battle Pyramid during Emerald's battle against Brandon. It soon disappears after being noticed by Brandon, Latios, and Latias, and Emerald. After the battle Emerald explains to the Frontier Brains that Jirachi can grant any wish and that capturing the Wish Pokémon is his true objective for challenging the Battle Frontier.
In Skirting Around Surskit I, Emerald and the Frontier Brains soon arrive at the Artisan Cave, where Emerald finds Jirachi sleeping. Jirachi awakens and unfolds itself, releasing a blinding flash of light. Emerald consults with Crystal on which type of Poké Ball to use and kicks a Timer Ball at Jirachi. Right before the Timer Ball connects with the Wish Pokémon it is sliced in half by Guile Hideout's sword. Jirachi attempts to flees, with Emerald chasing after it. Emerald then sends out Bonee and Monlee and has Monlee use Mach Punch to prevent Jirachi from moving by threatening to attack with his super fast punches. While Monlee keeps Jirachi distracted, Bonee whips out a pair of nunchaku made of bones. Bonee throws the nunchaku, which spin around Jirachi and binds its body, while not hurting it in the process. With Jirachi tied up, Emerald throws a Luxury Ball and aims for the line on Jirachi's stomach, as that is where its most vital energy might be. The Ball connects but couldn't shut due to Guile's Surskit's Psybeam and was then destroyed by Guile's sword. Before Guile can capture Jirachi it escapes from the cave, leaving it with four more days awake.
In A Cheeky Charizard Change-Up II, Noland reveals that he has found a way to track Jirachi by using the security cameras around the Battle Frontier to look for a flash of light Jirachi gives off when using Wish. Soon after this, Jirachi uses Wish on top of the Battle Dome's roof. Guile makes it to the roof first and captures Jirachi in a Poké Ball, with the Frontier Brains helpless to stop him. Guilde then flees to the top of Battle Tower to have Jirachi grant his wish.
Once there, Guild attempts to have his wish granted but is unable to figure out what is needed to have Jirachi obey him. In The Final Battle I, Archie steals the report that Professor Oak wrote about Jirachi from Noland. Realizing what he was missing, he has his Surskit force Jirachi's third eye open and makes his wish. Words form on Jirachi's wish slip, signifying that it granted Archie's wish. Suddenly, the water outside the Battle Frontier shoots into the air and begins taking shape, turning into a gigantic, monstrous Kyogre-shaped creature that towers the entire Battle Frontier. Archie reveals that his wish was to create a sea monster that will devour everything in its path.
After his wish has been granted, Archie tosses Jirachi to the side since it's too weak to be used in battle against the Pokédex holders. Emerald saves it from the chaos of the battle and the Pokédex holders agree that he should use a wish to unpetrify the Kanto Pokédex holders and Silver. Emerald makes his wish, but has trouble getting Jirachi's third eye to open. After Emerald accepts his feelings towards Pokémon, Jirachi opens its third eye for him and grants his second wish, unpetrifying the Kanto Pokédex holders and Silver.
Once realizing that Jirachi can grant more wishes, Archie takes back Jirachi and has it use Doom Desire against Emerald's Dusclops. With the delay on the attack, Poli pushes Dusclops out of the way and takes the damage from the move. After Archie is defeated, his body disappears and Jirachi is released.
In Epilogue, Scott revealed that he used Jirachi's final wish, wishing for many visitors to come to the opening day of the Battle Frontier. Jirachi is then seen floating towards the sky, preparing for its next thousand-year sleep.
Jirachi appears in a flashback in With a Little Help From Hitmonchan, where Crystal recalls her encounter with the Wish Pokémon.