Second Assault on Tokyo Settlement

Background
By forming the United Federation of Nations, the world is basically split between the UFN and Britannia. Immediately, numerous war fronts spring up, with equal gains and losses on both sides. In order to break the stalemate (and for UFN to liberate Japan), the leaders of UFN and Britannia had determined that they need to secure Area 11, particularly the Tokyo Settlement.

The Battle
Lelouch, after successfully capturing the attention of the nearby Britannian forces, which included the Knight of One, Bismarck Waldstein, and the Knight of Ten, Luciano Bradley, directed the Ikaruga to surface from the ocean and head towards the Tokyo Settlement with a small aerial armada, initiated the first part of his plan- he activated Gefjun Disturber trains positioned all around the settlement, disabling all Sutherland and Gloucester units in the vicinity. With the Britannian forces in the area rendered immobile, Lelouch then dictated the second part of his plan, which was for The Black Knights to uphold aerial superiority against any opponents that made themselves known whilst Rolo's infiltration team rescued Nunnally.

Schneizel then made himself known by bringing his own fleet into the fray, consisting of the Avalon, the Glaston Knights, Edgar, Claudio and David, in Gareths, and numerous Vincent Ward Frames, along with Suzaku's Lancelot Conquista. Luciano and his Valkyrie Squadron, having come from Kagoshima, also entered the battle, and other Rounds, namely Gino Weinberg and Anya Alstreim, provided support. Lelouch, who was overseeing the operations of the Black Knights and Rolo and Sayoko, was attacked several times, and ardently defended by Jeremiah and Guilford, who was under Lelouch's Geass effect.

The battle dragged on, with the Black Knights' battle line reaching its limit. Many Gefjun trains were destroyed, allowing Sutherlands and Gloucesters to re-enter the battle and thus outnumbering the Black Knights. Zero Squad Commander Kinoshita was shot down by a lone Vincent Ward, his ejection pod slamming into the side of a building and sprayed with gunfire. The reinforcements for the Black Knights were down to a single team led by Tamaki, and the situation as a whole got worse when the Mordred assaulted the Shinkiro and almost drained Lelouch's Frame of its power reserves for its shields, and then got chaotic when the members of the Valkyrie Squadron restrained an unaware Lelouch, and Luciano confronted him immediately afterwards.

Elsewhere, though, thanks to Sayoko saving Kallen from a planned execution, the Guren S.E.I.T.E.N. had broken free, slamming through David T. Darlton's Gareth in the process, allowing him to be taken down by Chiba. However, the situation for Lelouch was still a bad one, with Luciano using his drill to chip away at the Shinkiro's shield. Hope came, however, when Tamaki and his team interrupted Bradley with rocket fire. However, Tamaki's group was swiftly destroyed by a salvo of missiles, and Tamaki himself was forced to eject. Lelouch saw an opening, but Luciano quickly turned back and shattered the Shinkiro's laser crystal. Lelouch braced himself for the end, but all of a sudden Luciano stopped his attack, moving away from the Shinkiro as a purple blur quickly struck all four members of the Valkyrie Squadron, killing Liliana Vergamon, Marika Soresi and two others before the most of them had even realized they had been hit. The blur, revealed to be the SEITEN then focused its attention on Luciano's Percival. Kallen, driven to defeat Luciano, systematically destroyed his Frame's weapons until she vaporized the Percival, and Bradley, with a blast from her Frame's radiation surger arm.

With Luciano dead, Lelouch ordered Kallen to head for the Government Building. Suzaku entered, stepping in their way. Guilford tried to pursue him, but was stopped by Gino's Tristan. Meanwhile, Tohdoh and his group were launching an assault on the Avalon, which resulted in the death of Edgar N. Darlton. Lelouch then received a communication from Sayoko saying that Nunnally had been found, whilst Rolo had come across a transport craft (unknown to him, containing Miss Romeyer instead of Nunnally) and commandeered a Sutherland, and ordered Kallen to deal with Suzaku. Kallen, focusing on Suzaku, proceeded to outdo and utterly ravage the Lancelot Conquista, with Suzaku being insistent on fighting despite warnings from Lloyd and Cecile. Nina, all the while, pleaded with Suzaku to fire the F.L.E.I.J.A..

Suzaku realized that he simply couldn't win, and was about to surrender himself to death when his 'Live' Geass activated, compelling him to fire the F.L.E.I.J.A. at the Guren SEITEN. Kallen dodged it, but the firing of the weapon prompted Claudio Darlton to order all remaining Britannian forces to retreat. Chiba gave the same order, and urged Asahina, who was going after Rolo, to exit the Government Building. The warhead detonated in full, however, resulting in the atomization of the building, the deaths of Romeyer and Asahina, and the presumed demise of Sayoko and Nunnally (later saved by Oldrin). Lelouch himself was in the blast radius, but was saved by Guilford, who still thought he was Cornelia, who urged him to live on. With the detonation of the F.L.E.I.J.A, the battle effectively ended with a ceasefire.

Aftermath
A majority of Tokyo Settlement, along with 25 million people, perished under the F.L.E.I.J.A. attack. During such chaos, Britannia had sent an envoy, Schneizel, who exposed Zero as Lelouch vi Britannia. Thus, the Black Knights negotiated a truce with Britannia without approval from the UFN, and attempted to execute Lelouch. However, his escape forced the Black Knights to release information to the public that Zero was killed during the Second Battle of the Tokyo Settlement.

Negotiations may have started on the subject of freeing Japan from Britannian rule, but their extent and result is unknown. Given the death of Emperor Charles, Schneizel's disappearance, and Odysseus's unwillingness to assert control over the throne throughout the next month, negotiations certainly never completed. Despite this, UFN control over the area seems total after the following month, suggesting that Japan was effectively captured by the Black Knights during the lack of Britannian leadership, both in general, and in Japan specifically.

This is the last battle of the Second Black Rebellion.

Trivia

 * The human damage caused by FLEIJA on the Tokyo settlement (10 million civilians killed and 15 other million wounded) are similar to those (between 11 and 13.6 million dead and 10.3 to 14.6 million wounded) that could actually caused a Tsar Bomba (the most powerful nuclear weapon existing) if it were to be dropped on the real city of Tokyo, according to the website Nukemap.