With Professor Birch
Sceptile first appeared as a Treecko in Trying to Trounce Torchic, as one of the two Pokémon that was in Professor Birch's bag. When Ruby was rescued by Sapphire from a pack of wild Mightyena, she took him to her Secret Base. He thought she was a Pokémon of some sort, and was shocked to the spine when she started talking. The two ended up getting into a fight after he ordered Nana to Bite the supposed "Pokémon." Still holding his own Pokémon from fighting back, he phoned Professor Birch on the Pokégear that was in his bag, and was told to choose the "blue Pokémon," which he then chose over the "green one", finding Mudkip better than Treecko in terms of appearance.
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 him from Birch, a wave hit the tree, washing Treecko and a Pokédex away.
In Talk About Timing, Treecko, the bag holding Treecko and the Pokédex eventually made its way to Route 131, where it was found by Wally. After saving him, Wally had his Pokémon nurse the exhausted Treecko back to health.
In Dreadful Dealing with Dusclops, during Wally's 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 was not 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 Grovyle and broke through the black hole with Leaf Blade, defeating his opponent in the process.
In Rayquaza Redemption I, Wally was tasked with awakening Rayquaza on the peak of the Sky Pillar. Grovyle battled the Sky High Pokémon and 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 he quickly evolved into his final stage, Sceptile. There, he was knocked unconscious and captured by Guile Hideout, who planned to smuggle him 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 in Gotcha Where I Wantcha, Glalie. 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 him back under his control. Emerald then proceeded to use Sceptile to beat Noland's Golem with a single Leaf Blade. Sceptile next went up against his Glalie. Noland has Glalie use Crunch, which not only attacked Sceptile with its teeth, but froze his arm with Glalie's ice-cold breath. Glalie retreated and fired an Ice Beam from its eyes, which Sceptile dodged with Detect. Glalie is then commanded to use Sheer Cold, making a direct hit. Despite being hit by the powerful move, Sceptile gets back up with no clear injuries. Glalie soon starts faltering, and it is shown that Glalie was hit with Leech Seed, which Emerald reveals was put on earlier in the battle. Sceptile then hits his opponent with an Iron Tail, defeating Glalie and winning the battle. Emerald decided to sneak Sceptile out of the Factory and keep Sceptile as his own due to his suspicion that he is not an actual rental Pokémon.
In Chipping Away at Regirock, Sceptile participated in Emerald's challenge against Brandon and his Regirock in the Battle Pyramid. Sceptile managed to get the upper hand by absorbing Regirock's health with Leech Seed, but was knocked out by an Explosion. When Emerald's other Pokémon were defeated and Brandon looked like the winner Sceptile comes in and knocks out Regice with Iron Tail. Emerald soon reveals that he used a Revive to bring Sceptile back.
In Sneaky Like Shedinja, Sceptile participated in the Battle Arena to battle against Greta's Heracross. Sceptile attacked with Leaf Blade, but Heracross managed to deflect the attack with its horn. Sceptile then rushed in to deliver several punches and throws it to the ground. Greta has Heracross send Sceptile flying with Megahorn, heavily damaging him. The battle ends, and with an assessment, Greta's Heracross defeats Sceptile with a score of five to one.
In Susceptible to Sceptile, Sceptile battled against Ruby's Feefee in the semifinal round of the Battle Dome. Sceptile starts with a barrage of attacks, one of them paralyzing Feefee. This activates her Ability Marvel Scale, making most of Sceptile's attacks useless. Sceptile is then frozen by Feefee's Blizzard. Although frozen, Sceptile manages to regain its lost memories, giving it the strength to break through his icy prison and defeat Feefee, giving Emerald the win. With his memories returned, Sceptile began attacking Ruby, as he was furious over when Ruby called Mumu better than him 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.
In The Final Battle III, 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 Omega Alpha Adventure 3, Sceptile, alongside Chic and Mumu, trained under Ultima in order to fully master the ultimate moves. The training was issued by Steven Stone and Mr. Stone as part of a plan dedicated to preventing a giant meteoroid from crashing into the planet. With a set of Mega Bracelets and Mega Stones obtained from Steven, Sceptile gained the ability to use Mega Evolution. After a day of training, Sceptile fully mastered Frenzy Plant and attained his Mega-Evolved state.
With the training over, Mr. Stone had everyone taken to the Sea Mauville for the next stage of the plan. There, Sceptile and Chic were put on a set of machines known as the Absorber and ordered to coat themselves in the power of the ultimate moves. Once ready, Mr. Stone and Steven active the Absorbers, which proceed to painfully drain the life energy of Sceptile and Chic. The energy was converted into Infinity Energy and used to power a device called the dimensional shifter capable of warping the meteoroid to another location.