As a Treecko, Sceptile was one of the three starters Professor Birch was giving out to new Trainers. During the battle between Groudon and Kyogre, Birch became trapped on top of a tree in an attempt to get away from the flood. Before the Trainer that Treecko was promised to could arrive to receive it from Birch, a wave hit the tree, washing Treecko and a Pokédex away.
The bag holding Treecko and the Pokédex eventually made its way to Route 123, where it was found by Wally. After saving it, Wally had his Pokémon nurse the exhausted Treecko back to health.
During his climb of the Sky Pillar, Treecko returned the favor by saving Wally from falling off a crumbling floor. On the last floor, Wally encounters a wild Dusclops, which threatened to suck everything into a black hole it created. Although reluctant since it wasn't his Pokémon, Wally decides to trust in Treecko's power and sends him out to face the Beckon Pokémon. Immediately upon being sent out, Treecko evolved into a Grovyle and broke through the black hole with Leaf Blade, defeating its opponent in the process.
When Wally was tasked with awakening Rayquaza on the peak of the Sky Pillar, Grovyle was used to battle the Sky High Pokémon. With a powerful Bullet Seed, Grovyle broke through Rayquaza's ozone barrier, awakening it. The impact sent both Wally and Grovyle flying, separating the two.
Grovyle eventually landed on some island, where it quickly evolved into its final stage, Sceptile. There, he was knocked unconscious and captured by Guile Hideout, who planned to smuggle it and several other Pokémon to drive out the media in preparation for his capture of Jirachi. The shock of these events caused Sceptile to block them out of his memories, but he still retained an interest in the Pokédex.
Sceptile was put into the Battle Factory, where he was eventually found by Emerald in his battle against Noland. Immediately upon being sent out, Sceptile went on a rampage, and began attacking Emerald. Emerald manages to calm Sceptile down with his E Shooter, bringing it back under his control. Emerald proceeded to use Sceptile to beat Noland's Golem, and after some trouble, his Glalie as well. Later, Emerald decided to keep Sceptile, as he finds out that it was level 51, indicating that it's not a rental Pokémon, which are supposed to be level 50.
During his run in the Battle Pyramid, Emerald used Sceptile in his battle against Brandon, where it faced his Regirock. Sceptile managed to get the upper hand by absorbing Regirock's health with Leech Seed, but was greatly damaged by an Explosion. When Emerald's other Pokémon are defeated, Sceptile is used to defeat Brandon's Regice with a super effective Iron Tail. When Brandon asks how Sceptile came back, Emerald revealed that he used a Revive on Sceptile when Brandon got distracted.
During Emerald's challenge of the Battle Arena, Sceptile was used to battle Greta's Heracross. The battle lasted three turns and had the result determined by score, which had Heracross named the victor.
During the Battle Dome challenge, Sceptile is used to advance Emerald throughout the tournament. Eventually, it goes up against Ruby's Feefee in the semifinal round. Although frozen by a powerful Blizzard, Sceptile manages to regain its lost memories, giving it the strength to break through its icy prison and defeat Feefee, giving Emerald the win. With its memories returned, Sceptile began attacking Ruby, as he was furious over when Ruby called Mumu better than it in terms of appearance.
After losing to Tucker, Emerald challenged the Battle Palace next. When Emerald learns that Guile Hideout had captured Jirachi, Emerald left Sceptile, Sudowoodo, and Dusclops to battle Spenser by themselves while he went to face Guile. Later, Latios returns Emerald's Pokémon, along with the Spirits Symbol they had won in the battle.
During the final battle with Guile, Emerald is given one of the bangles possessed by Ultima. With it, he teaches Sceptile the ultimate Grass-type move, Frenzy Plant. With the power of Frenzy Plant, Sceptile teams up with the Pokémon of the nine other Pokédex holders to destroy Guile's monster Kyogre with a powerful Frenzy Plant, Blast Burn, Hydro Cannon, and Volt Tackle combination.
In the Omega Ruby & Alpha Sapphire chapter, Sceptile, alongside Chic and Mumu, trained under Ultima in order to fully master the ultimate moves. The training was issued by Steven Stone in order to prepare the three starters to learn Mega Evolution and prevent the ultimate moves from going out of control due to the increased power Mega Evolution provides. After a day of training, Emerald and Sapphire managed to successfully Mega Evolve their starters.