After the war, the Freedom was repaired and hidden in a secret underground base in Orb, where it laid dormant for more than two years. It returned to action during an assassination attempt on Lacus, when Kira launched in the Freedom and swiftly defeated the assassins' UMF/SSO-3 ASHs. Afterwards, Kira used the Freedom to "kidnap" Cagalli from her wedding and brought her aboard the Archangel before the ship left Orb. Later, Kira used the Freedom in two failed attempts to stop the battling between Orb and ZAFT forces during the Battle of Dardanelles and the Battle of Crete. During the Battle of Berlin, the Freedom fought and destroyed the Alliance's GFAS-X1 Destroy Gundam, resulting in the death of its pilot, Stella Loussier.
Shortly thereafter, ZAFT launched an attack against the Archangel, known as Operation Angel Down. At the battle's climax, the Freedom was stabbed in the abdomen by Shinn Asuka in his ZGMF-X56S/α Force Impulse Gundam with the Excalibur anti-ship sword from the Sword Silhouette. However, Kira managed to shut off the unit's nuclear reactor before losing consciousness, successfully preventing a nuclear explosion. His sister, Cagalli Yula Athha, later rescued him and the remaining torso of the Freedom from the waters using her MBF-02 Strike Rouge.
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