Thymilph, one of the Four Divine Generals of the mysterious Spiral King, arrives to support Viral's Enki, with the massive mobile Gunmen fortress, the Dai-Ganzan. Kamina and Simon pilot the Gurren-Lagann against seemingly overwhelming odds.
Having temporarily stalled Viral and Thymilph in the last skirmish, the Team Gurren and their newly arrived allies join forces as "Team Dai-Gurren" and launch a decisive strike against the regrouping Gunmen force.
Team Dai-Gurren managed to take control of the enemy fortress, but is still mourning their fallen comrade, especially Simon. After falling off a cliff, he notices a Gunman throw a capsule into a deep valley. Simon inspects it and finds he is able to open it with the same drill key he uses to pilot Lagann, and inside is a young human girl named Nia, but their introduction is cut short when an enemy Gunman appears.
Having been temporarily spared by Adiane, another of the Four Divine Generals, Team Dai-Gurren uses the reprieve to reassess their situation. Nia learns of Kamina's significance in Simon's erratic behavior and offers him some stinging, yet honest advice, which draws the ire of an untrusting Yoko. With tension building within the Team, the crew scrambles to stand by Nia's side when Adiane returns to complete her stalled attack.
Team Dai-Gurren falls into a trap set by the third member of the Four Divine Generals, Guame. The Team is taken captive and stored underground to await execution. While digging an escape path, Simon finally understands Kamina's last words to him and after having a discussion with Guame, Nia finds out the reason why she was thrown away.
During the following seven years, a new civilization rises and prospers under Simon's leadership. However, these peaceful times come to end when the threat mentioned in Lordgenome's last words starts to reveal itself.
After the Anti-Spirals' first attack and Nia's astonishing announcement, Simon looks desperately for her, while Rossiu finally completes his secret project.
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.
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