When she was small child, Crystal trained on Mt. Mortar to improve her skills in Pokémon catching. A wild Arcanine suddenly attacked and surprised Crystal, causing her to fall off a cliff and injure herself. When she awakened, Crystal found her broken arms wrapped in bones and covered in medicine. She soon discovered that a group of wild Pokémon that were also attacked by the Arcanine came to her rescue and patched her injures. When the Arcanine reappeared, Crystal noticed that the right side of its face was injured. With the help of the wild Pokémon, Crystal healed Arcanine's injuries and befriended it. All of the Pokémon then decided to join Crystal's team.
Crystal is first seen at her workplace, at Earl Dervish's Pokémon Academy in Violet City. She is hired by Professor Oak to help his Pokémon research by capturing Pokémon to fill up her Pokédex. She agrees to help the professor under the condition that he help repair the Dervish's rundown academy, which was later fulfilled.
After capturing all known Pokémon in Cherrygrove City and giving them to Oak, Crystal departs on her journey. After leaving, Professor Elm complains that he wasn't able to meet with Crystal and give her his Chikorita. Disappointed, Elm tells Chikorita that since Crystal already has a full team of Pokémon, she wouldn't want Chikorita on her team anyway. Angered by this, Chikorita attacks Elm and runs off to try find Crystal. Chikorita follows Crystal all the way to Route 30, where it attempts to convince her to let it join her team. Although she initially finds its too weak in comparison to her other team members, Chikorita's determination impresses Crystal enough to let it join her team. Crystal nicknames her new teammate Megaree and has it and Chumee switch places on her party. Upon arriving at Violet City, Crystal is shocked to discover the Pokémon Transporter System is down for the entire Johto region. She decides to call Professors Oak and Elm to inform them about her situation and that she found Megaree and added it to her team. Afterward goes to the outskirts of Violet City to capture more Pokémon. There, she meets Bill, who gives Crystal a portable transporter so that she may be able to transport her captured Pokémon to Professor Oak even while the normal Transporter System is down.
Crystal continues her journey by traveling through Union Cave in order to get to western Johto. There, Crystal is attacked by a group of Magneton that knock her unconscious and accidentally drop her into a submarine. Crystal later awakens and finds the owner of the submarine, Lt. Surge, is currently being held in place by a group of wild Corsola. Crystal helps Lt. Surge by finding and capturing the leader of the Corsola herd, causing the rest to let go. As thanks for saving him and an apology for accidentally kidnapping her, Lt. Surge takes Crystal to Olivine City on the S.S. Aqua.
Upon arriving, Crystal passes by the Battle Tower, a future attraction that is still under construction. A septic tank from the construction bursts, causing waste to spill out. Crystal manages to save the workers, but the waste spills into the sea, causing a wild Qwilfish to be enraged. Crystal captures the Qwilfish, but soon discovers another Qwilfish in danger of dying from absorbing the waste. She tries to take the Qwilfish to the Pokémon Center, but is startled by the appearance of Suicune. Suicune uses its powers to purify the sea and heal the sick Qwilfish. After it leaves, Crystal becomes enamored with Suicune and sets out to capture it. With the Pokémon tracking system on her Pokédex, Crystal begins following after Suicune in hopes of managing to capture it.
On Route 39, Crystal continues following after Suicune's trail. There, she encounters Eusine, another person who is aiming to meet Suicune. Due to their similar goals, Eusine declares Crystal to be his rival. Later, Crystal and Eusine encounter Suicune, but it turns out to be Ditto in disguise sent by Team Rocket to throw them off of the real Suicune's trail. After defeating the Ditto, Crystal and Eusine realize that someone must be after Suicune and set off to stop them. Crystal uses Parasee's Spore to put the pursuers to sleep and help Suicune to escape. Crystal and Eusine then set off to help Suicune, but Eusine leaves to face the pursuers while Crystal continues following after Suicune. Crystal tracks Suicune and arrives at the Burned Tower, where she battles to try and capture it. Despite her best efforts, Crystal is unable to capture Suicune and is defeated. After Eusine comes to help her, Crystal realizes that Suicune's goal was to meet with its master, Ho-Oh, at the Bell Tower. Coming to the conclusion that she prevented Suicune from achieving its goal, Crystal breaks down crying for failing to understand Suicune's intentions and getting in its way.The shock at her failure causes Crystal to lose her confidence in capturing, causing her to fail capturing even weak Pokémon. On Route 42, Crystal meets with her mother, who was passing by at the time.
After being told about her daughter's worries, Crystal's mother slaps sense into her daughter. Crystal's mother tells Crystal to re-train herself back from the beginning. Crystal agrees and heads to Mt. Mortar, where she first began training to kick Poké Balls. There, Crystal has an encounter with a wild Larvitar, which was the cause for Archy's injury in the past. Crystal battles the Larvitar and manages to capture it, regaining her confidence in the process.
Crystal training from the beginning
Crystal returns to Olivine in order to find a way to Cianwood City. There, she meets Yellow and her uncle, Fisherman Wilton, who take Crystal across the sea in Wilton's boat. While on the way, Yellow reveals that she was the one who awakened Suicune, Raikou, and Entei from the Burned Tower. Although initially suspicious of Yellow's claims, Crystal calls Professor Oak who reveals that what Yellow said is true and that he sent the two to help Crystal on her journey. The travel is interrupted by the appearance of Lugia, who begins attacking the boat and destroys it. Crystal is saved by the appearance of Gold and Silver, the other two Johto Pokédex holders that had been missing for some time. The three battle together to try and stop Lugia, but their attempts to defeat and capture it end in failure due to someone else capturing it first.
Under Professor Oak's orders, Crystal and Gold are sent to the Indigo Plateau, where the opening ceremony of the Pokémon League is being held. Their mission is to determine which of the Kanto and Johto Gym Leaders is actually the true identity of the villainous Masked Man. As they watch the Gym Leaders from each region battle each other in an exhibition match, Gold realizes that they are spied on. Crystal and Gold head into the League's stadium control room, where they meet Carl and Sham, the Masked Man's most trusted minions. Crystal and Gold manage to defeat the villains, but end up locked inside the control room while the Masked Man's army of Team Rocket Grunts invade the stadium via the Magnet Train. Crystal and Gold manage to escape from the control room, but find themselves too late to stop Team Rocket's invasion. With the Gym Leaders trapped on the Magnet Train, the Masked Man appears, having managed to capture both Ho-Oh and Lugia. Crystal and Gold face the two Legendary Pokémon in battle, but are unable to fully defeat them. The Masked Man gets tired of the battle and proceeds to attack Kurt and steal his scroll on making Poké Balls. With the scroll and the Rainbow and Silver Wings from Ho-Oh and Lugia, respectively, the Masked Man begins creating the GS Ball in order to achieve his goal of capturing time itself. As he heads towards his destination, the Masked Man is attacked by Misty, Blaine, and Lt. Surge, the three Gym Leaders that Suicune, Entei, and Raikou teamed up with. They battle the Masked Man to try and stop him, but are eventually defeated, allowing the Masked Man to escape and continue with his plan. Despite the heavy injuries it sustained during the battle, Suicune decides to team up with Crystal to chase after the Masked Man.
With Raikou and Entei following, Crystal and Suicune track the Masked Man to his destination, the Ilex Forest. They are soon joined by the other Pokédex holders, Red, Blue, Green, Yellow, and Silver. They battle the Masked Man, but are overwhelmed by his army of ice dolls. The Masked Man reveals that in their previous battle, he left Gold trapped in a wall of ice and left him inside the Crack in Time. The Masked Man uses the GS Ball to capture Celebi and heads inside the Crack in Time via the Ilex Forest shrine. With the Rainbow and Silver Wings in Yellow's hat, Gold is freed from his prison. Crystal, Gold, and Silver team up with Suicune, Raikou, and Entei and chase after the Masked Man inside the Crack in Time.
As they travel through the time stream, Crystal, Gold, and Silver see scenes of their various adventures. They eventually meet with the Masked Man and bear witness to a tragic moment of his past that led to him pursuing his goals in the present. When Crystal confronts the Masked Man about his motives, the Masked Man gets angry and knocks the Rainbow and Silver Wings away, causing Crystal, Gold, and Silver to be affected by the Crack in Time's pressure. Gold manages to retrieve the feathers, but gives them to Crystal and Silver. Gold sends Crystal, Silver, Suicune, Raikou, and Entei back to the real world while he goes off to fight the Masked Man alone. After landing, Crystal joins the other Pokédex holders in sending an attack inside the shrine to help Gold defeat the Masked Man.
After Gold defeats the Masked Man, the Pokédex holders celebrate their victory, only to find that Gold has not returned. They fear that he died, only for Gold to appear and reveal that he managed to survive. With the battle over and the villains defeated, the Pokédex holders returned to their normal lives. Crystal continued her job with Professor Oak and revealed to him that she managed to fill up her Pokédex completely. Professor Oak is impressed to hear of Crystal's success, but decides to hide the fact that more species of Pokémon keep appearing.
Crystal during the sixth chapter
In the sixth chapter, Crystal works alongside Professor Oak in helping save the five Pokédex holders that were turned to stone at the end of the FireRed & LeafGreen chapter. They send Emerald to the Hoenn Battle Frontier so that he may capture the Mythical Pokémon Jirachi so that its wish granting powers can be used on the petrified Pokédex holders. Due to lacking Pokémon of his own, Emerald battles through the Battle Frontier with Pokémon Crystal supplied with him.
On the fifth day of the Battle Frontier's opening ceremony, Crystal and Gold arrive at the Battle Frontier to help Emerald battle against Guile Hideout, a villain who is also after Jirachi. By the time they arrive, Guile had already captured Jirachi and used it to create a gigantic Kyogre-shaped monster made of seawater. Together with Emerald and the two other Hoenn Pokédex holders, Ruby and Sapphire, Crystal and Gold face Guile in battle.
While she and Gold distract Guile, Crystal instructs Emerald, Ruby, and Sapphire to train in an invisible room created by her Mymee so that their Pokémon can learn the ultimate moves Frenzy Plant, Blast Burn, and Hydro Cannon. They are eventually defeated, but managed to stall Guile long enough for the Hoenn Pokédex holders to finish their training. After Emerald manages to have Jirachi reverse the petrified Pokédex holders' condition, all ten Pokédex holders team up to battle Guile one last time. With a combination of a triple Frenzy Plant, Blast Burn, Hydro Cannon, and Volt Tackle, the ten Pokédex holders destroy Guile's sea monster, finally defeating him for good. With Guile defeated, the Pokédex holders celebrate their victory and decide to participate in a tournament at the Battle Dome. Crystal also participates, but is defeated by Green in the first round.
Afterward, Crystal goes back to Professor Oak's lab to perform maintenance on the Pokédexes. As she stares at photos of Emerald's adventure, Crystal flashes back to Guile's last moment. As Guile frantically tries to find his special suit of armor, Crystal and Emerald try to interrogate him on who gave him the suit in the first place. Guile attempts to reveal the identity of the person who gave him the suit, but disappears in a flash of light before he can finish his sentence. Although worried at the possibility of more evil in the world, Crystal shrugs off her thoughts and calls Professor Rowan from the Sinnoh region to help with the Pokédex maintenance.
Crystal in the ninth chapter
In the ninth chapter, Crystal takes a ride in her mother's helicopter to the Safari Zone for a field trip with the children from Earl Dervish's Pokémon Academy. Angered at the outfit her daugther is wearing to the trip, Crystal's mother forces Crystal to change into an outfit more suitable for the occasion. Later, while on the trip, Crystal meets up with Silver and Eusine. After Silver informs Crystal that Team Rocket had returned, Crystal leaves the children in Eusine's care while she goes to join Silver.
After they arrive at Route 38, Crystal and Silver are attacked by Ariana, one of the Four Generals that lead the revived Team Rocket. Ariana uses her Arbok to pin Silver to a tree, preventing him from help Crystal battle her. After freeing himself, Silver uses a plate to save Crystal, but is forced to leave in order to prevent Team Rocket from getting their hands on the Plates. Ariana eventually manages to defeat Crystal and is soon joined by Proton, Petrel, and Archer, the other Generals. Their appearance is followed by the arrival of the Mythical Pokémon, Arceus. Realizing that Team Rocket aims to capture Arceus, Crystal decides to stop them by trying to capture Arceus herself. Despite her best efforts, Crystal is unable to capture Arceus and is defeated.
After Arceus leaves with Team Rocket following after it, Silver returns with all sixteen Plates. He finds Crystal unconscious and in a tree and takes her to the Ruins of Alph, where Gold is battling with Arceus. Upon arriving, the Plates react to Arceus's presences, allowing Crystal, Silver, and the Four Generals into Arceus's barrier. With the Plates in the near vicinity, Arceus opens the portal to the Sinjoh Ruins. After the Johto Pokédex holders awaken, they go inside the ruins to find the Four Generals attempting to drag Arceus onto the Mystri Stage. Crystal, Silver, and Gold fight to stop the Generals' plan, but are stopped by Ariana, Petrel, and Proton. With the Plates, Archer forces Arceus to create the Legendary Pokémon Dialga, Palkia, and Giratina. Silver attempts to keep Team Rocket distracted while Crystal and Gold use Megaree, Exbo, and Feraligatr to destroy the Legendary Pokémon before they are fully formed with the ultimate moves. The attack successfully destroys the Legendary Pokémon, allowing Arceus to defeat the Generals and take back the Plates into its body. Despite this victory, Arceus begins reforming the Legendary Pokémon in order to enact its revenge on humanity.
After Dialga, Palkia, and Giratina fully form, everyone is surprised by the arrival of Lance, who has brought Pryce and Giovanni with him. The three former antagonists battle each of the three Legendary Pokémon in order to prevent them from battling each other and causing destruction to the Johto and Sinnoh regions. Crystal and Silver go to help fight against the Legendary Dragons while Gold stays behind to battle with Arceus. After Gold manages to calm Arceus down and stop its rampage, Arceus transports everyone out of the Sinjoh Ruins. Dialga and Palkia force Giratina back into the Distortion World and leave for the Sinnoh region.
With their journey over, The Johto Pokédex holders celebrate their victory and proceed to go their separate ways.