Red first met Pika at Pewter City in Wanted: Pikachu!. Pika had been causing havoc at the market, evading capture with his electric attacks and eating the shops' food. Red manages to capture him with help from Saur and attempts to befriend him, but to no avail. In the next chapter Red attempts to rely on Pika to help him fight the Pewter Gym, only to be refused. During his battle against Brock Red has no choice but to sent Pika in due to Poli and Saur being too tired. Brock orders his Onix to use Rock Throw on Pika, who dodges every rock except one, infuriating him. He then attacks Red prompting Brock to believe Red's wins before have been nothing but dumb luck. Brock angrily orders Onix to use his most powerful move, Skull Bash. The rock snake forms a twister before launching himself towards Pika. Diving, Red rescues him just in time. Pika, finally understanding Red a bit, launches a huge electric attack at Onix, which destroys him, earning Red the victory.
In Raging Rhydon, Pika is used in Red's first battle against a member of Team Rocket, facing off against a grunt's Rhyhorn. Rhyhorn begins with Rock Throw and manages to bury Pika, only for Pika to recover and fire a blast of electricity, surrounded by electrified debris from the Rock Throw. The attack successfully knocks out Rhyhorn, but then Koga appears and injects a liquid that forces Rhyhorn to evolve into Rhydon. Rhydon stomps on Pika before moving in to finish Red, but Pika slides out from underneath Rhydon having charged himself tremendously. Using his tail, Pika cuts off a huge portion off the cave roof, blocking the cave and allowing Red a chance to escape.
In A Tale of Ninetales, Pika is accidentally traded to Blue alongside Poli and Saur. During the three days that Blue has them he trains them vigorously. During his time under Blue's ownership he battles against a Ninetales, using his new Toxic attack to deal massive damage. They later traded back, while keeping the serious attitude that Blue installed in them.
In Meanwhile…Vileplume!, Pika is used in Red’s Gym battle against Erika and her Vileplume in his fight to save Eevee. Vileplume starts with Petal Dance, which Pika dodges. Vileplume then switches to Swords Dance and sends its petals flying straight for Pika, wrapping it up firmly and reducing its health to dangerously low levels. Through the petals binding his body Pika releases an energy clone from Substitute, which Vileplume easily defeats. Erika mocks Red for his futile strategy, but Red grins and points out that while Erika and Vileplume were distracted, Pikachu had already reached the machine holding Eevee. Erika is impressed with Pika's resolve and promises not to hurt Eevee anymore.
In Peace of Mime, Pika teams up with Blue's Golduck in order to break into Saffron City. Pika uses his Substitute to get past the barrier and Golduck uses Confusion to pass the information back to their Trainers. Inside the city Pika runs into the one who created the barrier, a Mr. Mime. Despite Mr. Mime's evasive attempts, a coordinated Thunderbolt from Pika successfully faints the Barrier Pokémon, lifting the barrier. Pika was later used in Red's fight against Lt. Surge, but was unable to do anything due to insulation he had in his suit.
In Long Live the Nidoqueen!?, Pika is used as Red's last resort in his battle against Giovanni. Due to Red having an insulated glove Pika was able to charge up his attack before being sent out, which allowed the two to surprise attack Giovanni and Nidoqueen, giving them the victory.
In A Charizard…and a Champion, Pika and Poli helped Saur defeat Blue's Charizard in a brilliant strategy by having Poli's water vapor and Pika's electric energy create a thundercloud that struck a vine shot and wrapped around him by Saur.
In the Yellow chapter, Pika is used in Red's battle against Bruno and his Hitmonlee. Red attempts to have Pika use Thunder Wave on Hitmonlee's knees to immobilize it, but misses due to the fact that Hitmonlee's knees are impossible to locate. After the battle is stopped Red is frozen and Pika was the only one to escape from the Kanto Elite Four. He managed to find his way back to Professor Oak's, beaten and wounded. Soon after, a girl by the name of Yellow comes in looking for Pika and tells Professor Oak that Pika is coming with her to look for Red. Yellow quickly heals Pika's wounds and the two set out to find Red.
In Cloystered, Yellow uses Pika in her attempt to escape from Lorelei. She first puts Pika inside a Poké Ball and then sends him out to spy on Lorelei and her tactics. After being reeled back in, Yellow storms out into the open and has Pika attack with Thunder Shock, which renders her Cloyster useless. Pika is later used in Yellow's first battle against Lance in Breath of the Dragonair Part 3. Pika launches himself at Lance but Lance throws Pika back to Yellow and has his Dragonair wrap around Yellow, immobilizing her. Pika tries to attack Lance, but stops when Dragonair's Hyper Beam narrowly misses him, although the beam changes direction and hits Pika anyways. Lance then has his Dragonair drop Yellow and wraps around Pika. Yellow tells Pika to use Substitute, and Pika creates a double that attacks Lance but misses. Enraged, Lance has his Dragonair use Dragon Rage, and Dragonair blasts Yellow, Pika, and its double, making them fall into the ocean. While underwater, Pika ends up learning Surf. Pika returns to the surface and uses Thunderbolt on Lance, causing a giant explosion and causing Lance to disappear.
In Double Dragonair, Pika is once again used to battle against Lance. Pika begins by saving Yellow from a pool of lava by using Surf. Pika then fires off an attack at Lance, but Lance counters with a powerful Hyper Beam. Yellow follows up by telling Pika to use Thunderbolt on Lance's Dragonite, while Lance commands Dragonite to use another Hyper Beam. Eventually Yellow becomes unable to stand up against Dragonite's attacks and has Pika's surf in order to create a whirlpool around Lance, attempting to trap him inside. Lance then uses Dragonite to fly through the lava and rams into Yellow and Pika. After the hit Lance disappears. During the final fight in The Legend, Yellow orders Pika to focus his energy into the ultimate attack: MegaVolt, sending a massive blast of electricity into Lance and defeating him. After the battle Pika finally reunites with Red.
Pika with Chuchu and their Egg
In Forretress of Solitude Pika is seen seen next to Yellow's Pikachu, Chuchu, with the two of them getting along well. In the next chapter Red heads off to Mt. Silver in order to treat the wounds he received from the Elite Four. Pika is left with Yellow and Chuchu because he doesn't want him to feel responsible for his injuries. Yellow explains to Pika that she, Chuchu and her Uncle will be heading to Johto, and invites Pika to join them. They head off for Johto together.
In Playful Porygon2, Pika and Chuchu produce an Egg together at the Day Care. During their stay the Day Care is attacked by members of Team Rocket and Pika and Chuchu are forced to flee with their egg. After escaping they are caught by the Masked Man and are held as hostages to intimidate Gold. Gold manages to free them and hatches their egg into a Pichu, named Pibu. In The Last Battle XIV, Pika participates in taking down Pryce and rescuing Celebi.
In PSs1, Pika goes with Red and Gold to Mt. Silver to help train his son. During the training Pibu is kidnapped and Red and Pika rush after the kidnapper, a Poliwrath and Venusaur. Due to their high level and being same species as Poli and Saur, Pika has trouble facing his opponents. With encouragement from Red Pika manages to defeat the two and rescue Pibu.
In Double Dealing with Deoxys, Red used Pika alongside Aero as his last two Pokémon in his battle against Blue. Red had Aero use Take Down on Scizor, which dealt no recoil damage due to his Rock Head Ability. Aero followed up with Dragon Claw on Scizor, so Blue switched him out for Rhydon. Seeing an opening, Red has Pika attack Machamp with an electric attack. To Red's surprise, the attack is suddenly redirected. Blue smirks and reveals that Rhydon has the Lightningrod Ability, which causes all Electric-type moves to be redirected towards it. Since Pika's Electric attacks had no effect, Pika jumps into the air and delivers an Iron Tail onto Machamp's head. The battle then ends in a tie.
In The Final Battle III, it is revealed by Gold that Pika wasn't inside his Poké Ball during the Pokédex holders' petrification, and was thus able to escape alongside Chuchu. Pika is seen wearing Red's hat and using Surf to get to the Battle Frontier to see Red get recovered, while Chuchu is seen flying with her balloons to get to the same destination (wearing Yellow's straw hat). Pika later learned Volt Tackle along with his partner and offspring and used it against Guile Hideout's fake Kyogre, helping to defeat it.