- On his deathbed, Fleet Commander Fairlock entrusts Ridget with Gargantia. Meanwhile, Amy is sad when Melty and Ledo abandon the ship.
- The people of Gargantia are split between those who wish to stay with Ridget and live in peace, and those who are wanting to explore the historical ruins with Pinion by destroying a whale-squid nest.
Commander Fairlock, surrounded by his fellow superiors, is lying on his deathbed. Knowing his fate, he passes his command to Ridget before passing away.
Chamber is able to confirm Earths coordinates in relation to the fleet; however, this discovery comes with the realisation that returning to the Alliance is impossible.
[Opening Credits]
The people of Gargantia attend the public funeral for Captain FairLock. There is tension between The Shipmasters and Ridget, as some consider her unfit for the position.
Pinion convinces Ledo to join his treasure venture by telling him about a whale squid nest.
Flange and Ridget discuss the treasure mission. Flange intents to go to salvage historical information and plans to take those Gargantian civilians who wish to leave.
Melty tells Amy and Saaya that she will leave with the new fleet. Amy finds out that Ledo plans to leave as well.
The fleet commander is being laid to rest. Flange and the Shipmasters bid farewell.
Ridget is alone in her apartment and looks at an old photo of her family and Fairlock. She leaves and finds Pinion in the hall. Pinion asks Ridget to sign paperwork for their departure. She declines.
Amy finds Ledo making his flute. She decides not to talk to him and leaves.
Amy is looking over Gargantia. Saaya flies in and discusses Amys dilemma. Saaya suggests that Amy should go with Ledo. Amy decides to stay to look after her brother.
Ridget is stressed about her new position. Bellows discusses her leadership of the excavation team with Ridget.
Amy is at home and making dinner for Bevel. They discuss Ledo leaving with the new fleet. Amy is hurt by Ledos decision to leave.
[Advert break]
The separation begins as the ships of those deciding to leave begin to depart. Some decide to stay.
Flashback: Ridget and Fairlock discuss how to deal with an unknown boy. Fairlock allows the boy to decide himself.
Present: Ledo is sharpening his blade on Chamber in the hanger. Bevel runs down to try convince Ledo to stay on Gargantia. Ledo says he will not, but gives Bevel his special flute. Ledo talks about how destroying the Hideauze will help protect Earth from becoming like the Alliance.
Ridget arrives to Fairlocks memorial. She places sand on his body before he is launched into the depths of the ocean. Ridget makes a speech to the people of Gargantia and informs them that she has been chosen by Fairlock to be the new commander. She promises her loyalty to her people and asks for their assistance. Just before Bellow speaks up, others begin to show their support.
Ledo arrives at Amys house. He tells both her and Bevel that he is leaving. Bevel promises to look after Ledos flute until he returns.
Amy and Bellows stand on a metal wharf. Bellows informs Amy of her general disapproval of those who have decided to leave. Amy looks towards the ocean and appears sad.
[End Credits]
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