Sigma is from a future where the Mavericks are at war with the Maverick Hunters, who exist to stop the Mavericks. Growing bored with the war, Sigma eventually learns about the Heroes of Legend and their status as the Creator through some ancient texts. Uninterested at first, Sigma eventually notices Bass' article, and learns of Bass' origin as a robot. Realizing that Bass is the key to his victory, Sigma decides to go back in time so he can infect Bass with the Maverick Virus, essentially becoming a god in the process. Sigma eventually perfects his time machine and sends himself and Vile, his second in command, into the past, unaware that Zero and Axl, two long time enemies of Sigma, followed Sigma into the past.
Upon arriving in the past, Sigma and Vile are recruited by Ghirahim as members of the Revolutionaries, a group intent on usurping the Creator and remaking the world as they see fit. At some point, Sigma finds out that not only has Zero followed him to the past, but has also joined the Revolutionaries. Later, Sigma is ordered to infiltrate the Neo Smash Champion Tourney, resulting in Sigma joining Ghetsis and Kefka Palazzo as a member of Team Chaos. Sigma is also indirectly responsible for Roy joining the Brawl Spectator Society, as he told Roy that he shouldn't snoop around as if he has authority.
At the start of the tournament, Sigma and Kefka interrupt the confrontation between the Heroes of Legend and Team Metal, which consists of Mecha Sally, Ridley, and Ino. Sigma then arranges a Battle Royale between the Heroes of Legend, Team Metal, Team Chaos, and Team Corruption, consisting of Sasuke Uchiha, Samus Aran, and Fawful. During the match, Sigma fights against Bass and Marth, but leaves with Kefka after Mecha Sally initiates her transformation into her Metal Overlord form.
Later, Sigma and Team Chaos assist Team Metal during the conflict on the Egg Carrier under Mephiles the Dark's orders. However, Sigma and his teammates retreat after the Heroes of Legend return to Subspace, but not before Sigma learns that Bass is no longer able to be infected by the Maverick Virus thanks to Zero.
Later, Sigma and Team Chaos head to Subspace after Wolf O'Donnell, who is a member of the Revolutionaries, organizes a match there. During the match, Sigma and Team Chaos are betrayed by Mephiles, who sends them away to an unknown location. Sigma later returns to Earth after Mephiles is defeated, and returns to the Revolutionaries' HQ after Team Chaos disbands. Despite the fact that Bass can no longer be infected by the Maverick Virus, Sigma is unphased by the loss, as he realizes he can simply infect Mecha Sally instead, seeing as she has already amassed an army of robots under her control. After Mecha Sally defeats Sonic the Hedgehog at Seaside Hill, Sigma decides to betray the Revolutionaries and put his own plans into action, and ambushes Mecha Sally, Sonic, and Sasuke with Vile's help. During the conflict, Sigma reveals to Mecha Sally, Sonic, and Sasuke that his ultimate goal is create a world where robots reign supreme, and that Mecha Sally is the key to his plan's success. Despite Mecha Sally's resistance, Sigma manages to infect her with the Maverick Virus. However, Sigma's plan backfires when Mecha Sally refuses to obey him. Unphased by this setback, Sigma boasts that while he can't control Mecha Sally, Ghiraham can't control her either, before he retreats. Sigma later returns with his entire legion of Mavericks, still determined to control Mecha Sally, and follows Mecha Sally's army into Subspace. However, Sigma is intercepted by Ike and Zero, the latter having betrayed the Revolutionaries. Refusing to give up when he is so close to victory, Sigma and Vile battle against Zero and Ike to settle things once and for all, but ultimately retreat after the Heroes of Legend's transformation into pure Phazon. Sigma later attempts to possess Mecha Sally in order to finally achieve his goal of a world inhabited by robots, but somehow merges with Mecha Sally's programming, effectively killing Sigma in the process. However, Sigma is later revealed to be alive, although his soul is apparently eradicated after Mecha Sally purges him from her body. Despite this, Sigma managed to survive, but has been usurped by Vile due to his apparent death. As a result, Sigma liberates Wolf O'Donnell and King Dedede from prison, stating that they have lost everything and the only way to rise back to power is to join forces, which Wolf and King Dedede agree to. Sigma then declares that the war has only just begun, and dares the Heroes of Legend to come and get him. During The Dimensional War, Sigma rejoins The Revolutionaries, but abandons them again after his defeat at Sasuke Uchiha's hands, and joins Mecha Sally's army as she initiates her own rebellion, and is present when Mecha Sally unveils the Mecha Series, consisting of Infinity Titanium Mecha Sonic, Mecha Knuckles, Mecha Ino, and the roboticized and weaponized version of Gwen Tennyson. In Season 36, Sigma is modified by the Revolutionaries so that he can access any of his other bodies at will, becoming stronger than ever. In Season 38, Sigma oversees the liberation of Fawful and later intercepts the reborn Heroes of Legend after they follow the Revolutionaries to their hidden base, attempting to convince the Heroes of Legend that destroying Master Hand will not affect the Smash World in any way as Kabuto Yakushi's actions have allowed the Smash World to evolve to the point where they no longer need a Creator.
Sigma's primary appearance is based off his original appearance in Mega Man X.
In Season 38, Sigma uses his appearance from Mega Man X5 so that he is better suited for combat.
Sigma, as a Maverick, believes that humans are inferior to robots and wishes to exterminate them. Having grown bored of the war in his own time, Sigma wanted to infect Bass with the Maverick Virus in the past so he could usher in an age where robots reign supreme, essentially becoming a god in the process. However, after Bass becomes immune to the Maverick Virus, Sigma has decided to infect Mecha Sally with the Maverick Virus instead, since she already has an army of robots at her disposal.
Sigma is a master manipulator, as he was able to fool Ghetsis and Kefka into believing he was on their side and was able to fool the Revolutionaries into believing he was loyal to their cause, while in reality Sigma had his own motives in mind.
Like Ghirahim, Sigma always has a back up plan, as after Bass became immune to the Maverick Virus, Sigma merely decided to infect Mecha Sally instead, since she is full of potential.
Due to being from the future, Sigma believes the technology of his time is superior, as he was impressed at Mecha Sally's design despite being from a "primitive" time.
One thing that sets Sigma apart from other villains is his persistence. No matter how much his plans fail, Sigma is determined to make a world where robots reign supreme.
In Season 38, Sigma reveals that while he resents the Heroes of Legend for helping their friends destroy Kabuto and preventing Sigma from achieving his own vision of an ideal world, he also respects the Heroes of Legend as they remind him of how he was before being infected by the Maverick Virus. Sigma also claims that while he felt the same pain that the rest of the Revolutionaries did when the Heroes of Legend died from the Kabuto Virus, he won't hesitate to stop the Heroes of Legend from ruining their plans.