* Episode 4, "Gravestone On A Frozen Field", ends with one of these. After finding a wrecked UN ship on a moon of Saturn, Susumu and Mori are sent to investigate. It turns out to be [[spoiler:the ''Yukikaze'', Mamoru's ship, which was supposedly destroyed in the opening battle at Pluto. They managed to survive, and no one came to help them until it was too late and the Gamilans captured them.]]
* Erich Domel's death, motivated by his will to not make his men's deaths senseless. The ''Yamato'' surviving, thus making ''everything'' a SenselessSacrifice, only makes it worse.
* "A Clockwork Prisoner": Analyzer re-activates a Garmillan android soldier in order to study it. He ends up befriending the curios automata, which he names "Alter". Later, Alter curiously peeks into the mainframe of the ''Yamato'' and finds a "goddess" [[spoiler:(who is actually Yurisha)]] and goes to any length to pursue it. To protect the ''Yamato'' from a hack attack, Analyzer is forced to put Alter down. The episode, as a whole, goes to great lengths to explore the question of WhatMeasureIsANonHuman.
* Celestela's death.
* [[spoiler: Yuki]]'s death. Especially for how [[spoiler: Susumu]] reacted: [[StepfordSmiler having it kept a secret to not sadden the crew and feign not suffering]]. Thankfully, [[spoiler: she]] [[BackFromTheDead got better]], courtesy of [[spoiler: Mamoru Kodai activating the Cosmo Reverser just for that]].
** And that leads right in something terrifying: [[spoiler: now the Cosmo Reverser won't work anymore, [[AllForNothing and the whole voyage was useless]]]].
** And this is corrected by the last link of this chain: [[spoiler:[[HeroicSacrifice Okita willing himself to die to reactivate the Cosmo Reverser]].]]
* How the war started in the series: [[spoiler:the Gamilan ships appeared at the edge of the system for a peaceful contact when [[ColonelKilgore Serizawa]] [[WeComeInPeaceShootToKill ordered to attack without even talking]], Okita refused and was removed from command, and when Shima's father followed the order the Gamilans destroyed his ship and killed him]]. What's worse is that [[spoiler:due to political necessities it was said that the Gamilans opened fire first, [[KarmaHoudini meaning that Serizawa got away with causing a]] HopelessWar, the loathing Shima and many others have for the Gamilans is completely unjustified]], and the Gamilans, who are trying to force Earth into surrender, have absolutely no idea why the Terrans don't do just that and refuse the demands of surrender they send before any engagement.
* Earth three years after the return of the ''Yamato'': once the environment was restored, the government went back on Okita's promise and started building ships with Wave Motion Guns, using [[spoiler:a time rift generated by the Cosmo Reverser]] to build the new fleet faster, and started a colonial expansion, and when Teresa of Telezart sent a request for help it was ignored, with Hijikata ReassignedToAntarctica for his efforts to have the ''Yamato'' mount a rescue mission. The crew of the ''Yamato'' rightly asks: where is the Earth they fought to restore?
* Despite the fact that there is now peaceful coexistence between Humans and Gamilas now, there are still signs of racial tension among the Humans. In a FreezeFrameBonus, a robot is seen quickly scrubbing off ''"Gammies, get out!!"'' from a nearby wall on a public town road.
* How the crew of the ''Yamato'' answered to the situation above: they went to Telezart anyway, stealing the ship and committing high treason for justice, while also going back on Okita's promise and restoring their ship's Wave Motion Gun to have a chance to succeed.
* When Gatlantis makes their attack on Planet 11, Nagakura of the Space Calvery comes to the rescue of one of the Gamilan Colonists, a young girl who was seen back in Episode 3 helping to decorate a Christmas Tree with several other kids; including her older brother; whom she said thought that the ''Yamato'' and her crew were heroes that would come to save them all. [[spoiler:Cue the waterworks when they come across her brothers' crushed body, only his left arm was visible from beneath the rubble; [[EmpathyDollShot reaching out to his]] ''[[EmpathyDollShot Yamato]]'' [[EmpathyDollShot Spaceship Toy.]]]]
* In the second season, Yuki regains her lost memories, but ends up losing all her new ones at the same time. Which means that she doesn't remember Susumu.