After the failure of the Giga Project, Bias publishes scores for each officer based on their past operations, grading their plans and results out of a maximum of one thousand points. Anyone who reaches a thousand is the elite of the elite, a so-called "Thousand-Point Brain". With this scoring system, everyone knows exactly where they stand, and to earn higher marks they all do their utmost, striving to become a Thousand-Point Brain.

Kemp, who has always seen himself as Bias's senior disciple, finds his score falling behind the others after several operations. Proud as he is, Kemp cannot bear the other officers' mockery, still less losing Bias's trust, so he has no choice but to strengthen himself again. Kemp has always been obsessed with beauty, believing everything must follow the principles of beauty. That is why he made himself a Beauty Beast, knowing it was not the strongest modification; he would rather give up strength for beauty. But the Beauty Beast's power is never enough in real combat, so he goes one step further and changes from a Beauty Beast into a "Fear Beast", a monster with a terrifying appearance but many times more powerful in every respect.

Kemp's further modification triggers a new modification plan for Mazenda. In her first modification she had turned half her body into machinery fitted with various weapons. This time she abandons her body entirely, keeping only her human brain, and fits even stronger weapons all over her body, such as a "five-finger machine gun", "palm cannon", "elbow rapid-fire cannon", "knee missiles" and "back rockets". A true killing machine, "Machine Mazenda", is born!

At this time, Jou and the others meet Gou Omura again, who has regained his memory. Gou tells them about Volt from the inside and reveals some of Bias's secrets. When he first joined Volt, he once strayed into an area Bias had strictly forbidden anyone to enter. In a mysterious room he found twelve strange devices, eleven of which held human brains. He saw with his own eyes Bias use the power of these brains and devices to turn from a decrepit old man back into his usual self. One device stood empty, as if waiting for one more brain. Gou was horrified, but he dared not ask, and kept it all to himself as a secret.

Guildos and Butchy, believed to be cosmic geniuses from outer space who joined Volt out of admiration for Bias, are in fact robots built by Bias to spur the other officers to work harder, a secret not even they know. Badly wounded in his final battle, Guildos discovers that his body is full of machinery and realises the truth; his energy exhausted, he is finally discarded by Bias. When Butchy learns the truth, his pride is shattered and he gives up on himself for a time. Megumi's singing encourages him to pick himself up, but this enrages Bias, who makes him explode.

In the end, even Ashura turns out to be just a pawn Bias created to train the other officers. The genius education Bias gave Arashi Busujima was really nothing more than artificial modification. After Ashura's all-out attack is defeated by Liveman, Bias decides he is no longer of any use; what is more, Ashura has accidentally discovered part of Bias's secret. Furious, Bias decides to destroy him. Ashura turns back into the old Arashi Busujima, a man so slow he cannot even work out eight plus four. But Busujima is still Busujima, and his courage is undiminished. As Liveman struggles against the Battle Brain, Busujima straps powerful explosives to his body, charges at the Brain Beast, and blows himself up together with it.

To become a Thousand-Point Brain, Mazenda uses the power of dreams to create the Nightmare Brain. Because it is created from dreams and has no physical body, even Super LiveRobo is defeated by it. Just as Mazenda is about to become a Thousand-Point Brain, Gou Omura arrives and reveals Bias's plot to take other people's brains. Bias has been planning all along to collect Thousand-Point Brains. With those brains he can not only stay forever young; once he has twelve Thousand-Point Brains, he can generate a "Giga Brainwave" that will hypnotise and control all humanity. Bias already has eleven, and needs only one more to achieve his ambition. He has been recruiting talented geniuses from everywhere as his disciples precisely to take their brains.

Hearing Gou's words, Kemp and Mazenda are shocked. Half-believing him, Mazenda stops her attack for a while, but after repeated encouragement from Bias she goes out again. Her fierce attacks leave the five warriors helpless, and Bias finally grants her the honour of the Thousand-Point Brain. But Gou was right: Bias has already sent Gash to the battlefield to take Mazenda's Thousand-Point Brain! Full of regret, Mazenda is no match for Gash, and only the intervention of Gou and Liveman saves her from losing her brain for now. But Gash pursues her relentlessly, and with nowhere left to run, Mazenda mechanises her brain as well, to end Bias's designs on it. Enraged, Bias punishes her, and she explodes in front of everyone.

Kemp, the last one left, decides to offer himself to Bias. He transforms into the Fear Beast, attacks like a madman and finally defeats Liveman, becoming a Thousand-Point Brain as he wished. After Gash takes his brain, Kemp's body turns into the Terror Beast Brain, while Yusuke follows Gash, slips aboard his shuttle and tracks him to Zuno Base. Colon arrives with LiveRobo as support, and finally Super LiveRobo defeats the Terror Beast Brain.

With the last Thousand-Point Brain in hand, Bias immediately broadcasts the Giga Brainwave to the whole world, and all humanity falls at his feet. Only Yusuke, who is on Zuno Base, escapes the hypnosis. He transforms into Red Falcon, attacks Bias and destroys everything. Struck down, Bias reverts to his true form as an old man, but using the power of Kemp's brain he becomes young again, as "Boy King Bias".

Zuno Base goes out of control and falls to Earth. The injured Boy King Bias meets Megumi, who cannot bring herself to hurt someone who looks so young; instead she hopes to use the chance to persuade him to make good use of his youth and start his life anew. Bias is unmoved by her words, but Kemp's brain comes to regret its life and chooses to destroy itself. Without Kemp's brain, Bias turns back into a feeble old man. Supported by Gash, he returns to Zuno Base, which is about to explode, and is destroyed together with it.

Seeing their former friends come to such an end, Yusuke and the others are filled with sorrow. Yet they know the Earth is finally at peace and that all their efforts were not in vain. And so the battle between Liveman and Volt comes to a close.