The 'Reign of Teridax' was the period compressed between the time after Teridax took over the Matoran Universe and his death at Bara Magna.
Nearly a month after Teridax took over the Matoran Universe robot, he is almost ready to leave to Bara Magna. Inside him, a Ko-Matoran named Mazeka, and another Teridax from another dimension, in which the Makuta are beings of light, continue their search at the Southern Continent. The two were in a ridge, from which they saw the remains of a Matoran village. Mazeka recognised it as a village of Ba-Koro though the corpses of the Ba-Matoran were nowhere to be seen. Suddenly, a strong wind threw Mazeka off of his feet, sending him down the mountain, but the alternate Teridax used his powers to stop it. However, Makuta made the ground beneath him erupt, breaking his concentration, and both fell. They landed hard on the ruins of the village where there were many corpses of dead Visorak scattered. Makuta started talking to them through a dead Visorak. The alternate Teridax confronted Makuta, who sent a three Shadow Takanuva, saying that they would give him a proper welcome to his universe.
Around this time, Makuta was sure that he had all rebellions controlled, and he started his voyage to Bara Magna.
Back in the Core Processor under Metru Nui, a battle still raged. Axonn, Helryx and Miserix, who though that the universe had to be destoryed, and Brutaka, Tren Krom possesing Lewa Nuva's body and Tuyet though that there should be another option, and fought. Miserix battled against Tren Krom, and confident that the being possesing Lewa's body would be weak, he knocked the Toa to the ground. However, Tren Krom used his mental abilities to counterattack, sending a massive mental attack at Miserix's mind. The attack nearly left Miserix brain dead, but Miserix had endured after millennia of torture, and slammed Tren Krom agains a wall. Helryx, sensing that the battle would surely turn Teridax's attention, and by thus killing the chances of her plan functioning, prepared to unleash a Water Nova Blast. Tuyet, seeing Helryx's intentions, grabbed Axonn's axe and slashed it at Miserix, making the Makuta fall on Helryx. However, at the last moment Helryx vanished from her position, and appeared behind Tuyet, and headlocked her. Then at the chamber's entrance Artakha appeared, and stopped the battle. Artakha first talked to Tren Krom in Lewa's body, and after Tren Krom refused to give up his new body, Artakha used his powers to swamp their spirits again, returning Tren Krom to his body and Lewa to his. Helryx then approahced Artakha, and siad that she could destroy the universe, and she would do so, but they were interrupted by Makuta, who sent the fighters, Artakha, Hafu and Kapura away to space. Lewa wasn't going to be teleported, as Makuta didn't want him to use his Air powers to help the others to survive, but Lewa grabbed Brutaka and he was too teleported. Once in the space, Lewa created bubbles of air around his companions, except for Miserix, who could survive without air. Artakha was about to teleport them all to Bara Magna, but before he could to so a dimensional portal appeared, and dragged them into it. They appeared on a forest. Kapura realized that the stone floor was moving, and the bricks of the wall behind him embraced him. Their saviour stepped in, and Miserix recognised him as Vezon, the insane half Skakdi who had helped in the mission to free him. Vezon revealed the pressence of an insane Great Being, who had ordered Vezon to save them. Then he revealed that they were on the jungle world of Bota Magna.
Nektann, a Skakdi warlord, decided to side with Teridax after the Makuta took over the universe, thinking that there was no point to oppose the universe. He was soon assigned with the task of crushing a rebellion in Metru Nui, but he and his army of Skakdi and Rahkshi found the resistance of the Toa Mahri.
Short time later, at the island of Zakaz, the five surviving Toa Mahri were sent by the Order of Mata Nui to spy on the Skakdi warlords, and see if they had allied with Makuta, like Nektann had recently done. Also, they had to investigate the reasons for why the Piraka had been taken away from the destoryed island of Daxia and brought to Zakaz. On the shores, Kongu absorved the air around the Skakdi guards that scouted the beach, knocking them unconcious. They then advanced, only to find an encapment of warriors surrounded by a thick wall of stone. Hewkii used his control over stone to make the walls explode, defeating the Skakdi there. They continued walking, and Hahli lead them to an underground water stream, which lead to some ruins. When they got out, they saw that a warlord and his Skakdi army were assembled around the ruins, and that he was giving a speech against Teridax. The warlord said that it was time for them to take control of the universe and overthrow Teridax, and that their salvation was emerging from underground. Then, a tank full of Energized Protodermis emerged from the earth. Inside it they threw a Zyglak, a Vortixx, a member of Krekka's species and, to the Toa Mahri's surprise, the five Piraka. However, a green cloud which came out of a lake also entered at the tank, and took part in the fusion process. When it was done, a powerful, golden being stepped out of the tank. It then talked to the Skakdi, telling them that it was hungry, and that it needed a meal, and that it would give power in return. Then the being altered the minds of the Toa Mahri, who wanted to serve the Skakdi, who they though that was a superior race.
On the devastated island of Karzahni, Pridak, had reached the limit of his patience. He first had though that The Shadowed One had succeeded into infecting Teridax with the virus, as he had noticed a small earthquake. However, though Pridak didn't know, it had been Teridax shooting off to space. He decided that he had to act, and finally he ordered his troops to march to Metru Nui.