After Nidhiki and Krekka were sent to Metru Nui and didn't return, "The Shadowed One" went to Metru Nui with Voporak and Sentrakh. Voporak, soon after their arrival, stole the Kanohi Vahi from Vakama and gave it to "The Shadowed One."
He later discovered that Teridax had absorbed and killed his Dark Hunters, and battled him for supremacy. However, during the fight, he was thrown into Voporak's aging shield, resulting in him aging over 3,000 years in moments. He survived this encounter and still existed in the time of the Toa Nuva, having sworn revenge on the Brotherhood and causing a war that had raged for at least 1,000 years and resulted in the mass deaths of Toaeverywhere.
He actually intended to kill Zaktan some time ago with his eyebeam power. However, something went horribly wrong, and Zaktan was transformed into his current Protodites condition.
At some point, he sent several Dark Hunters toward Voya Nui. It is unknown what became of them."The Shadowed One" faced a difficult decision during the invasion ofKarda Nui: to either keep all of his Dark Hunters fighting against theBrotherhood of Makuta or send half of them to go after the Mask of Life, leaving the other half vulnerable to attack.
He formed an alliance with the Order of Mata Nui and had blockaded Xiato prevent them from making weapons for the Brotherhood. He wanted to destroy them but Helryx ordered him not to.
While inspecting the destroyed factories, he found a Vortixx who was hiding something, and trapped him in crystalline protodermis, until he found out that he was hiding something in a chest. He opened the chest, and what he found inside was the Makuta viruses that Kojol brought to Xia, but lost. "Ancinet" found him, and "The Shadowed One" told him about what he had found. He had also killed the Vortixx hiding it, and then killed "Ancient" with his disintegration beams, since they possessed the knowledge that he had the viruses.
"The Shadowed One" then confronted BarrakiKalmah, Ehlek and Mantax in Xia's main factory. The Barraki suggested an alliance between the two factions, for which "The Shadowed One" demanded something in return. However, when he found out that the Barraki knew of the virus he had obtained and apparently knew how it was used, "The Shadowed One" eventually decided to take the alliance into consideration. at length he agreed to talk with the Barraki's leader, Pridak in Karzahni.
"The Shadowed One" was one of the survivors of Mata Nui's death in The Kingdom Alternate Universe. After they all moved to the island of Mata Nui, "The Shadowed One" became a part of a ruling council of the newly founded Kingdom of the Great Spirit.
Some time after the takeover of Metru Nui by the Toa Empire, a small force invaded Odina, but "The Shadowed One" managed to escape with the help of Toa Naho. He then went into hiding. His staff, however, was somehow claimed, and later placed in the Archives as a trophy.
The Shadowed One survived the Doom Event, and transported himself to our main dimension to seek help. However, he landed on Bara Magna, and wandered off into the Deserts. He was then transported to an unknown place.