Nine years before the Masked Man's uprising, he stole six children, which would help him in researching time for his goals. Entei, Raikou and Suicune swore to stop him, and succeeded in breaking his control over Ho-Oh he captured. For this, the Masked Man cursed them and sealed them hidden away in the Burned Tower.
By accident, Yellow entered a rock in the Burned Tower, where she was in a strange space. The Legendary Beasts - Suicune, Raikou, and Entei - appeared before her, thanking her for opening the way to their freedom. Yellow told this story to Crystal,, for she came to help the latter in catching the Legendary Trio.
Falkner and a Bird Keeper encountered Raikou, who was joined by Entei as well. The Bird Keeper wanted to catch both of them, but was nearly crushed by Entei. Falkner thought Suicune would visit him as he did some of the other Gym Leaders, but decided to take on these two instead. He had Skarmory use Swift, but missed both Legendary Pokémon. Raikou used Thunder and Entei Fire Blast, and the attacks hit Skarmory. Just as they went to repeat their attacks, Falkner anticipated them, as their attacks would collide and injure both Entei and Raikou, while Skarmory would use Agility to escape. Falkner threw his modified Poké Balls to catch Raikou and Entei, but Suicune appeared and used Bubble Beam, encasing the Balls. While Falkner was concentrated on battling Suicune, the latter was helped by Entei and Raikou to prevent being captured. Before the trio left, Suicune telepathically told Entei and Raikou about Ho-Oh's statue at the Tin Tower. Before challenging Suicune, Pryce explained to Whitney about Suicune's previous encounters with the Gym Leaders, and remembered how it used Bubble Beam to prevent Entei and Raikou from getting captured.
With Misty having obtained Suicune, Entei and Raikou would soon choose their own partner to battle against the Masked Man. Eventually, it joined Lt. Surge, as it saw something in common between them.
Lt. Surge had Raikou power up the train and change its direction back towards the Indigo Plateau. To stop the Masked Man, he joined Misty and Blaine, who had Suicune and Entei. Before leaving, Raikou left some of the electricity in the train system, which would later help Bill out in fixing the system and calling out for help. The trio encountered the Masked Man, who had Ho-Oh and Lugia in his possession. Ho-Oh fired an attack, but was stopped by Entei. To continue, Lt. Surge gave Raikou a Magnet, which powered the latter's moves up. During the fighting, the Legendary Beasts tried to persuade Ho-Oh to stop attacking, but failed. Instead, Suicune encased the Masked Man behind a crystal wall. The Masked Man broke out, and even if it had a hole in its stomach caused by Entei's fire attack, it blew it and Raikou away with ice.
After Misty was rescued, Entei, Raikou and Suicune joined Crystal and pursued after the Masked Man in Ilex Forest, where they joined the Pokédex Holders, who had their Pokémon fire attacks to finish the Masked Man off once and for all. The Masked Man, Pryce, stopped the attacks and summoned ice soldiers to stop them, and went into the time portal to find Celebi. To stop him, Gold, Silver and Crystal rode on the Legendary Beasts into the time portal. However, Gold stopped the other two, and had them travel out of the portal, since he wished to pursue after Pryce on his own. In the end, the Legendary Beasts scattered away.
Anabel, who caught Raikou, came with it to watch the exhibition match. She also had Raikou beside her to keep an eye on Emerald. It was also present at the infirmary, where Noland was resting. It was also present when Anabel and the other Frontier Brains questioned Emerald for taking Sceptile from the Battle Factory.
Facing an armored man in Artisan Cave, Anabel charged on her Raikou. Raikou used Thunder Shock on the armored man, to trap him, and even conjured a thundercloud inside the cave. To stop them, the armored man had his Surskit emit a sticky substance to trap them, preventing Raikou and others from moving. After the battle, Raikou, Anabel and others went to the Battle Arena, where Scott explained them more about the armored man, Guile. Anabel, who was with Raikou at the Battle Dome, explained to Emerald his challenge against Dome Ace Tucker was a tournament; they called out on many trainers to come, and promised they would protect the audience, for she and her colleges were the Frontier Brains.
Anabel faced Emerald in the Battle Tower, despite being possessed by Guile. Emerald valiantly fought against her, even if Raikou inflicted a lot of pain on him and his Pokémon. Soon after, Anabel fainted, and the battle was stopped. Raikou was with Anabel and the other trainers. It also met up with Gold, Silver and Crystal, its former allies.
Anabel's Raikou intimidated Team Aqua and Magma admins; they wanted to know where Zinnia was, but the admins replied she didn't say where she went to.
Due to the meteorite threat, the Frontier Brains, including Anabel and her Raikou, joined the other Gym Leaders and the Elite Four to stop the collision. Anabel's Raikou was used to launch an attack against the meteorite.
|Thunder||Really Raikou & Entirely Entei I|
|Spark||Really Raikou & Entirely Entei I|
|Thunder Shock||The Last Battle IV|
|+ indicates this Pokémon used this move recently.*|
- indicates this Pokémon normally can't use this move.
- ^ a b c CR054: The Last Battle IV
- ^ a b CR036: Buzz Off, Butterfree!
- ^ CR025: Hello, Lickitung
- ^ CR026: Really Remoraid
- ^ CR021: Really Raikou & Entirely Entei I
- ^ CR022: Really Raikou & Entirely Entei II
- ^ CR028: Savvy Swinub
- ^ a b CR053: The Last Battle III
- ^ a b CR063: The Last Battle XIII
- ^ CR055: The Last Battle V
- ^ CR062: The Last Battle XII
- ^ EM002: Swanky Showdown with Swalot
- ^ EM003: Interesting Interactions Involving Illumise
- ^ EM010: Chipping Away at Regirock
- ^ EM011: You Need to Chill Out, Regice
- ^ EM013: Skirting Around Surskit I
- ^ EM014: Skirting Around Surskit II
- ^ EM015: Sneaky Like Shedinja I
- ^ EM017: Verily Vanquishing Vileplume I
- ^ EM025: Facing Gulpin Is Hard to Swallow
- ^ EM035: Epilogue
- ^ ORAS017: Omega Alpha Adventure 16
- ^ ORAS021: Omega Alpha Adventure 20
- ^ ORAS022: Omega Alpha Adventure 21