To soothe the public opinion, Rossiu overthrows Simon and puts him under arrest. But when the Anti-Spirals launch a large-scale attack on Kamina City, he is left with no option but to let Simon engage the enemy using the Gurren-Lagann, not before resorting to extremes to put him under his control.
As Simon arrives in prison, he unexpectedly meets Viral, who comments on how far he has fallen. Meanwhile, the truth about Rossiu's emergency plan and the consequences for those left behind on Earth are revealed.
One year earlier, Yoko starts working as a schoolteacher on an island until she learns of the situation at Teppelin and returns to break Simon free. Once again reunited, Simon and the members of Team Dai-Gurren launch themselves into space to protect the Arch-Gurren from the enemy forces, now accompanied by Viral as co-pilot of the Gurren-Lagann.
The Gurren-Lagann and the Arch-Gurren join together to form the massive Arch-Gurren-Lagann and stop the Human Annihilation System.
The members of Team Dai-Gurren make their preparations for the imminent war against the Anti-Spirals, but Rossiu is missing. However, when Kinon tells Simon about what he really intends to do, both start to look desperately for him.
Guided by Simon and Nia's feelings for each other, Team Dai-Gurren break through dimensions in search for the Anti-Spirals' home world. But after falling into the enemy's trap, they end up losing some of their most precious members, due to its vicious offensive.
Team Dai-Gurren struggles to escape from the ocean of despair created by the Anti-Spirals without success, until history repeats itself, as another irreplaceable member of the Team sacrifices himself to save the others.
After finally transforming their flagship into the Super Galactic Gurren-Lagann, Simon and his friends successfully fight back against the enemy. When their enemy starts to use their own memories and desires against them, someone reappears to help.
At last, Simon and Nia are reunited, and by combining the power of its members, Team Dai-Gurren creates the galaxy-sized Tengen Toppa Gurren-Lagann, and engage the Anti-Spiral threat in a decisive battle to determine the fate of the universe.
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