Just because this game lives on in infamy doesn't mean it can't make you cry. And not just from [[ThatOneLevel some of the levels]].
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[[quoteright:350:https://static.tvtropes.org/pmwiki/pub/images/iblis_trigger.jpg]]
[[caption-width-right:350:[[OurHeroIsDead S-Sonic...?]]]]
* Elise's ImageSong, [[https://www.youtube.com/watch?v=zaUGQ673VbU My Destiny]], has sad but hopeful lyrics.
-->Stay close to me, my love\\
You've taught me that life can be revived\\
With this smiling face, the meaning of my destiny can be changed\\
For your love
* In Sonic's story, Elise apparently dies in the Egg Carrier's crash because [[YouAreTooLate Sonic couldn't reach her in time,]] which causes Sonic to have a moment of true despair, something we rarely see from him in his video games.
* Elise asking Sonic to remember Soleanna when he leaves is quite sad, given the game's reset button ending.
* The scene where [[HeroicSacrifice Blaze seals herself in another world with Iblis inside of her]] is surprisingly moving, considering [[{{Narm}} what many other scenes in the game]] are like.
* The scene with Team Dark on the beach. Despite Mephiles' attempts to turn Shadow against his friends, Shadow holds no ill will towards Omega, and Rouge comments that she'll always stand by his side. For a trio of [[AntiHero often-morally questionable loners]], they really are incredibly close.
** Shadow also seemed pretty upset when he first found out that the world would turn against him.
* Sonic leaving Elise at the end of the game.
* Sonic's murder by Mephiles. Sure, it may be {{Narm}} to some, but just the very fact our childhood hero was outright killed -- and so quickly and easily -- by a monstrous creature like him is enough to shake most long-time ''Sonic'' fans to the core. It's especially not helped by Mephiles [[KickTheDog cruelly laughing at Elise]] after he does the deed.
-->'''Elise:''' (''[[PleaseWakeUp desperately shakes Sonic's body]]'') Sonic! ''Sonic!'' ...Sonic? ''[scene cuts to a blackout of a young Elise collapsing in despair while her father's voice rings in her ears]''\\
'''Duke of Soleanna:''' Yes, Elise... Don't cry, no matter what happens. ''[scene fades to black before Elise's voice laments in despair]''\\
'''Elise:''' Oh... no... no... ''[scene fades back to her mourning over Sonic before giving out a SkywardScream]'' [[BigNo NOOOOOOOOO!]]
** It's more depressing when the other characters see the deceased blue hedgehog in front of them. A DarkReprise of "His World" starts playing as Sonic's friends and allies, even [[TheRival Shadow]] and [[AntagonistInMourning Dr. Eggman]], grieve.
--->'''Eggman:''' (''angrily and mournfully'') Mephiles played us all for fools! His plan all along was to cause the princess to be so consumed with despair that she'd cry.
*** Amy's reaction is a particular gut punch. Starts with her calling Sonic's name in disbelief (which cracks towards the end), after which she numbly falls to her knees, burying her face in her hands. Whether or not she's actually crying or not is up in the air due to a lack of graphics and the absence of sound, so all you can see is her just shuddering violently. It's much more effective than screaming and blubbering; that's ''anguish'' right there. [[FromBadToWorse To make things even worse for her]], she's the one who finds the '''''blue''''' Chaos Emerald at White Acropolis during the End Of The World level. ''[[PlayerPunch Ouch]]''.
*** Shadow, of all characters, [[ICantLookGesture refuses to look at Sonic's body and instead turns away and closes his eyes.]] He even unfolds his arms when no one is looking. Also, the bit when Silver says "So that's why, he [Mephiles] wanted me to kill Sonic before", all Shadow can do is turn away from Silver in guilt. He couldn't stop Mephiles in time before Sonic was killed, and it's like he's silently blaming himself for it... made even worse when you realise this isn't [[VideoGame/SonicAdventure2 the first time he tried and failed to protect someone.]]
*** Compared to the rest of the game, the voice acting in this final scene is quite good, almost to the point where it sounds like legitimate mourning.
*** The way Knuckles' voice cracks when he shouts Sonic's name is surprisingly tear-jerking. Even as one of Sonic's biggest rivals, [[VitriolicBestBuds he's still been one of his best friends since the early days]]; he knows what has happened immediately, and he's clearly devastated. In the Japanese dub, he says Sonic's name in a quiet tone but it's just as heartbreaking as the English version.
--->'''Tails''': [[LittleNo No...]] Y-you don't think...?
--->'''Knuckles''': ''SONIC!''
** It's more than just them mourning. Throughout the series, Sonic's always been the one to inspire others to take action. He's always been the one to say "we can do this!" or "let's go get 'em!" when things looked the bleakest. With Sonic dead, there's no one to keep up a positive attitude, no one to say everything's going to be fine... ''nothing''. And with the exceptions of Silver and Elise, everyone else starts to cross the DespairEventHorizon at the sight of their leader, their ally, their ''friend'' having been murdered. Couple this with [[TheBadGuyWins Solaris successfully forming]] and going on to almost destroy time itself with seemingly no one left to stop it, and this genuinely feels like one of, if not ''the'' DarkestHour of the entire franchise.
* [[TheVeryDefinitelyFinalDungeon End of the World]] plays music that reflects the mental state of each of the characters. While all are major tear jerkers in at least some way, the closest people to Sonic have especially painful implications all-round in the pace and instrumentation. They in particular are, [[OurHeroIsDead fittingly]], very reminiscent of the FiveStagesOfGrief:
** Tails' version[[note]]Denial[[/note]] is [[https://youtu.be/Q2DaIZBRP5w extremely bleak and empty,]] lacking anything in the background other than [[HellIsThatNoise a low, harsh buzzing hum.]] This, what he says (and ''how'' he does so) when starting the level[[note]]''"Sonic... we have to find the Chaos Emeralds soon!"''[[/note]] and obtaining the Emerald[[note]]''"Sonic, I'm coming!"''[[/note]], and the fact that his stage is '''Crisis City''' shows that [[HeroicBSOD Sonic dying has unhinged his long-time best friend massively.]] Even while trying to save him, it's [[BreakTheCutie left Tails feeling hopeless, frightened, and just completely ]] ''[[BreakTheCutie lost]]'' without [[HeterosexualLifePartners Sonic's usual kindness, support and encouragement]] even at the lowest of times.
*** In a CallBack to ''VideoGame/SonicAdventure2'', if Tails ends up being killed by an enemy or obstacle, he weakly mutters "So... nic..." as he tries and fails to get back up. Hearing this in [[TheVeryDefinitelyFinalDungeon End of the World]] ''hurts,'' just like losing to Eggman -- or defeating Tails ''as'' Eggman -- back in that game.
** Although not as sad or creepy as Tails', Silver's theme[[note]]Anger[[/note]] [[https://youtu.be/kCAeRQbefS8 just feels... dead inside.]] Considering Solaris just, in one fell swoop, [[DiabolusExMachina took away his ultimate victory over Iblis]], killed his new friend who helped him successfully do it -- and whom Solaris' previous form also [[CheatedDeathDiedAnyway nearly succeeded at tricking Silver into murdering]] -- and [[AllForNothing rendered Blaze's sacrifice ultimately for nothing,]] it can be assumed that Silver's [[TranquilFury pretty furious to say the least]] about all this. The emptiness of his theme implies [[DespairEventHorizon it may have gone even further.]]
** Knuckles' theme[[note]]Bargaining[[/note]] [[https://youtu.be/kb9TKKhUKwg has the least amount of revisions,]] though [[OminousPipeOrgan an eerie, funereal organ]] plays constantly alongside many, many drums. Knuckles has more at stake here than everyone else. Not only are the Chaos Emeralds he's been charged with protecting in danger of being lost ''permanently to time itself'', but [[VitriolicBestBuds one of the people Knuckles values most]] has [[ItsPersonal been murdered.]] This is his last chance to right the wrongs that have been done. If he can't, then reality itself will end; and it will end because he couldn't live up to his duty as Guardian of the Emeralds. He's angry, sad, and confused; the three worst traits to be approaching a problem with. But it's all he's got. And he'll dig to the depths of the Earth itself to save all of existence.... [[LastStand or die fighting back.]] The fact that the Echidna's emerald is '''Cyan''' doesn't help, as it most likely reminds him of his failure of protecting the Master Emerald, which is green.
** Amy's theme[[note]]Depression[[/note]] is [[https://youtu.be/01Abi1xZN7Q especially strained and downbeat]], mostly consisting of slow, hollow techno and [[OneWomanWail heartbroken female singing in the background.]] Seeing her long-time crush's dead body and [[MyGreatestFailure living with the knowledge that she couldn't protect him when she most needed to]] clearly hasn't helped her at all; especially not going by her searching for the '''blue''' Chaos Emerald in [[SnowMeansDeath the cold, lonely wastes of White Acropolis.]]
** Shadow's Theme[[note]]Acceptance, has ''highly'' evident undertones of Anger[[/note]] is [[https://youtu.be/c0zvUwhzH8U a chaotic mis-match of continuous, yet repetitive choir-backed beats]] that overlap. Shadow has spent the entire game fighting off Mephiles' machinations, while managing to survive the identity issues and angst that the creature's been tormenting him with. Now the world's greatest hero -- someone whom [[WorthyOpponent Shadow still respects deep down despite their bitter rivalry]] -- is dead, and time itself has reached the fringe of total collapse. The black hedgehog is running on a mixture of desperation and rage, especially since Sonic's death is [[VideoGame/SonicAdventure2 not the first time Shadow has tried and failed to protect someone he cares about]]. His Chaos Emerald being the often anger-associated '''red''' doesn't help.
* It's quite clear that because of her royal duties Elise has had very few friends in her life -- if any at all -- so seeing her only friend die in front of her is a bit much, but then she realizes that the only way to set things right is to lose the one person who likes her for who she is, not what. She's spent the better part of her life trying not to cry to uphold her father's last wish, but in that last scene she's crying; Creator/LaceyChabert does such a convincing job that any player will feel bad for her.
* The final scene of Silver's story. Silver and Blaze have defeated Iblis and Silver attempts to seal Iblis inside himself to prevent it from resurrecting itself once again. Unfortunately, he's rejected by Iblis. Blaze offers herself as a the vessel, since her soul is already filled with flames. As she does so she commands Silver to seal her in another dimension using Chaos Control. He refuses to, not wanting to lose her, and the two share a touching moment before Blaze floats into the sky, as her body disappears. Before she does a final blast blows away the volcanic soot-clouds allowing sunshine into the world for the first time in 200 years. Silver merely stares up at the sky as the credits begin rolling. Combine that with the awesome song that plays during the credits and you've got yourself a really sad ending. It's made even worse by the fact that Blaze is the only character who doesn't appear in the Final Story.
* Speaking of Silver, if his monologues are even close to reality, then he's basically a ChildSoldier. He was born after the rise of Iblis, and all he's ever known is a world where fire fills the sky and people search desperately for food and water, and fight hopelessly against a monster that cannot be destroyed in a ForeverWar.
* Sonic '06 had a LOT of parallels between stories about friendship/abandonment. As stated above, there's Elise gaining a friend in Sonic, then having to lose him for the fate of the world. There's Silver, who has to watch Blaze, his only friend who he spent his entire journey [[AmbiguousSituation die/disappear/travel-to-another-dimension]] for the good of the world, and then there's Shadow, who finds out the whole world will eventually turn against him, and the person responsible for his capture was none other [[EtTuBrute than one of his only two friends]], E-123 Omega. At least Rouge tells Shadow ''she'll'' never turn against him even if the world does... for all the good a deceased friend does in such a regard two-hundred years in the future, though.
* Watching Amy and Silver's new friendship [[BrokenPedestal nearly end up destroyed]] when Amy first learns Silver only wanted to find Sonic to assassinate him.
* Imagine you're just chilling in your own domain, minding your own business. Then out of nowhere, [[HumansAreTheRealMonsters a bunch of morons kidnap you and drag you from your realm and turn you into a lab rat, running experiment after experiment on you,]] [[EvilIsNotAToy trying to subjugate you and steal your power for their own selfish desires]]. Then you finally find a time to resist, only for it to result in you getting [[TheDisembodied split from your own body and most of your power anyway]]. You run off to catch your breath and figure out where to go from here when suddenly some other jerk decides to freeze your form. What happens next? [[AndIMustScream Solitary confinement]], stuffing you inside a container with no way out seemingly ever. Now you're strapped with nothing but your own pain, confusion, and rage to analyze, overthink, and let fester for years and years. [[StartOfDarkness This is the tale of Mephiles.]]
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