* The part when the Wolkenritter decide to undertake the completion of the Book of Darkness without Hayate's knowledge and against her wishes, made especially heart wrenching with this line
-->'''Signum:''' "Forgive us, our master. We shall be breaking our oath this one time... ''Please forgive us for this wrongdoing!''"
* Vita dragging herself across a desert on some distant planet, fighting monsters to fill the book despite her knight armor being ripped up and she's covered in bruises and cuts. Then her shoe rips and she falls over, getting a face full of sand.
-->'''Vita''': [[PunctuatedForEmphasis It. Doesn't. HURT!]]
** The Movie version of the scene makes it even more depressing by setting it after Hayate has been hospitalized [[note]]combining it with a scene from episode 8 where she and Zafira fought a Kraken[[/note]] and changing the location to a muddy hillside [[GrayRainOfDepression during a thunderstorm]].
--->'''Vita:''' I don't know if Hayate will be happy with becoming the true master of the Book. She might get upset. She might despise us. But... to see the kind Hayate suffering like that... I can't stand it. I can't stand losing Hayate!
* Everything that happens on the roof during episode 9. [[WhamEpisode EVERY]][[FromBadToWorse THING]]!
** Vita line before attacking Nanoha and giving birth to Nanoha's FanNickname.
--->'''Vita:''' Don't you dare interfere. Just a little longer, and we'll be able to save her! Hayate will become lively and joyful... she'll return to us! We've been working so desperately! There's only a little left, so... DON'T INTERFERE!
** The dialogue between Signum and Fate , when Signum [[NotSoStoic starts to cry]].
--->'''Signum:''' "Stop... We guardian knights decided we'd even throw away our honor to save our mistress' smile. ''You can't stop us!''"
** Hayate's BreakTheCutie moment. She is a 9 year old girl who has been alone and crippled for a good chunk of her life. Then she gets a family in form of the Wolkenritter and they live happily for six months. She even makes some friends. Her condition is slowly getting worse (causing her a great deal of pain), but she doesn't care so long as she has her family. [[spoiler: On Christmas Eve, she's teleported to the top of a building, only to see that two of her family members has been killed, and the other two disappear in front of her. What's worse, the culprits are her friends, who tell her that she's going to die. After going through that, it's a miracle that she didn't [[DespairEventHorizon completely break]].]]
*** The movie version is even worse. [[spoiler: Seeing your closest family member killed right in front of you by two of your friends is bad enough, but what about watching your entire family get ImpaledWithExtremePrejudice by the very thing that gave them to you?]]
* The eyecatcher from episode 10 shows a picture of Hayate with the Wolkenritter [[spoiler:who have just been absorbed into the Book of Darkness]], and one of the deceased Clyde Harlaown with Lindy and a young Chrono, while appropriately sad music plays in the background.
* Fate's time in the [[LotusEaterMachine Book Of Darkness' dream world]] in episode 11. She ''knows'' it's all just a dream, but when it hits home that, in this world, she is truly loved by her mother Precia ''and'' has Alicia as the sweet older sister she never knew, she breaks down in tears. And then later, as she prepares to leave the dream-world to help save the day, she and Alicia share a heart-wrenching goodbye, Fate crying and apologizing as Alicia calmly fades away into light [[FinalFirstHug in her arms]], her last words being of love to her sister.
-->'''Alicia:''' "It's all right. I'm your big sister, after all. Your strong and gentle friends are waiting for you, right? Then, take care... Fate... I wish... that we could've been like this in reality, too."
** ''How'' does Fate know this she is an a LotusEaterMachine? Because this reality is too nice to her... where "too nice" means "having a regular childhood". If that doesn't drive the point home how awful Fate's life until then has been and make you weep, nothing will.
** The movie version drives home just how much this is affecting Fate. In the original TV version, when she realizes this is the world she always wanted, she starts quietly crying and sniffling. In the film, once it sinks in she's inconsolably bawling her eyes out.
* The eyecatch in episode 11: Fate and Alicia asleep. Cute and sad.
* [[spoiler:Reinforce]] sacrificing herself to break the ViciousCycle in the last episode. As well as Hayate unexpectedly turning up and ''desperately'' trying to stop her. Made worse by the fact that this is the only time that Hayate's being in a wheelchair is played up as vulnerability instead of just a side effect of the Book's curse. She has all the power in the world [[spoiler: [[UselessWithoutPowers and she can't even save someone right in front of her]].]]
* Chapter 6 of the ''A's'' manga and it's animated version in ''The Movie 2nd A's''. Hayate starts crying after remembering [[spoiler:Reinforce]], then tries to hold back the tears, calling herself a crybaby. Nanoha and Fate, in perfect unison, stand up and hug her from both sides, telling her that she doesn't have to pretend to be strong in this case.
* The scene from the end of episode 3, where Bardiche and Raising Heart are throwing up error messages to the people trying to fix them, telling them they don't have the right parts. The missing parts they are referring to are named CVK-792, or the Belka Cartridge System that their enemies are using, which are incredibly dangerous in the first place, but are more so for devices that have not been designed with that system in mind. The episode ends with a rather tense and melancholy BGM, with the word PLEASE written across the center of the screen in large print in the devices distinctive rune-script.
* A retroactive example; the fate of Chrono's father elaborated on this season turns his speech to Precia in the first season about how the world is always filled with things that should never have been into an invitation to ManlyTears; he speaks to Precia from experience.
* Fate's attempts to rescue Nanoha during the first battle don't go as well in the movie. In fact, Signum ends up slamming her into the ground when she tries to rush at Vita. This leads to an IronicEcho of the rescue from the series as she drags herself towards Nanoha's unconcious body.
-->'''Signum:''' Is she your family or something? \\
'''Fate:''' She's my friend. We've been apart. I finally got to see her. ''(tears well up in her eyes)''.
** Signum is unable to look her in the eye as she drains her Linker Core, [[TheScream and Fate's screams echo across the city]], complete with a shot of Shamal and Zafira with looks of obvious guilt as they drain Arf's Core as well.