The story takes place in the weeks following the fall of Ba Sing Se, and takes on Katara's perspective as she chronicles the following events in her diary. Aang had been badly injured by Azula's lightning attack, and has fallen into a state of unconsciousness. Desperate, the gang and the Earth King have been forced to flee to Chameleon Bay, which is guarded by Katara and Sokka's father, Hakoda. The Fire Nation is sending in reinforcements and the Water Tribe ships will not survive another battle, so the Avatar and his allies must abandon the bay.
During this retreat, the Earth King departs the group to travel the country in exile with his bear, Bosco, and Pipsqueak and The Duke join the group after they were caught stealing food. Meanwhile, Katara heals the wounded Aang on a daily basis, still clinging onto her hope that he will soon revive.
During the retreat, the Water Tribe fleet encounters a Fire Nation scout ship, but does not stand a chance of winning the battle. Instead, Sokka proposes that they sink their own ships and hijack the Fire Nation vessel in an effort to protect Aang. The warriors agree and they sink their fleet, traveling to the shore in rowboats. After setting up camp for the night, the warriors storm the enemy ship the following morning, only to find that the crew is lazing about since they found the Water Tribe fleet destroyed. Thanks to Sokka, the crew catches on to the attack, but are quickly subdued with stink bombs and bending.
With the vessel captured, the gang dons Fire Nation disguises and decides to sail through the infamous Serpent's Pass, only to find that the one opening through the pass has been barricaded by a fortified Fire Nation gate. Hakoda, however, gains entry through the gates when he claims that they are joining the Western Fleet. It is here that they are told by the bridge staff that the Avatar is dead. Katara is traumatized by this belief, but Sokka states that this assumption means the Fire Nation will no longer hunt them down.
The gang continues their journey toward the Fire Nation, and Katara continues to tend to the unconscious Aang. The comic ends with her stating that the fight must go on, and that hopefully, the Avatar will return.
In the comic, the Southern Water Tribe ships are destroyed when Team Avatar and the others capture Fire Nation ships to use as a disguise, but in "The Day of Black Sun", the same Water Tribe ships are used again to transport the invasion force.
In the comic, Toph can clearly be seen using metalbending without direct contact in order to tie up the firebenders opposing her, whereas in the series she does not manage to do this until the finale because of its apparently greater difficulty.
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