History Heartwarming / ScoobyDooMysteryIncorporated

** Before this, when Shaggy struggles to ask Mai Lee on a date, Scooby finishes for him, encouraging in to do so. Clearly he’s trying to make up with his earlier behavior with Shaggy and Velma being in a relationship and actually cares about his best friends feelings. Velma also encourages him to RaceForYourLove to say goodbye one last time to Mai Lee after she leaves.

* For the twists and turns and depression that was episode 26, Mayor Jones rescuing Fred stood out for this troper and showed that even with all the abuse and neglect that he put him through, he still cared for Fred's safety.

** Then, after [[spoiler: said man-crab does, in fact, capture Daphne]], Fred goes into a HeroicBSOD. He spends ''hours'' digging, [[SugarWiki/FunnyMoments wherever he is]], including in the Mystery Machine and Velma's room, [[spoiler: since she was dragged under the sand at the beach]], and then spends the next several minutes making random comments about Daphne.

* Another moment in episode 15 is when [[spoiler:Maxwell]] kidnapped Velma and Scooby. He wants Velma to [[spoiler:hack into the National Train Database]] and he gets her to do this by threatening Scooby's life by hanging him from tree over a cliff with sharp rocks at the bottom. When he's about to drop him Velma begs him not too and agrees to his demands. The dialogue explains it all.

* Velma, to [[spoiler:Mai Lee after she's been caught]] in Episode 18:
-->'''Velma''': He's too good for you! Dog issues or no dog issues!

* For the twists and turns and depression that was episode 26, [[spoiler:Mayor Jones]] rescuing Fred stood out for this troper and showed that even with all the abuse and neglect that he put him through, he still cared for Fred's safety.
** Becomes even more HeartwarmingInHindsight when it turns out [[spoiler:that in spite of [[EnemyWithin his good side being sealed away by the curse]], [[AdultFear hearing his son cry out for help because he was about to die]] was [[PapaWolf enough to break him out of the curse]] albeit temporarily]].

* Daphne returning Judy's locket to her in "Hodag of Horror", which greatly touches Judy. [[spoiler: It becomes something of a {{Tearjerker}} when, at the end of the episode, Professor Pericles instigates Judy and Brad's FaceHeelTurn, meaning that such touching moments with them won't be happening again.]]

* The fact that [[spoiler: almost everyone in Crystal Cove, even the imprisoned villains from Mary-Ann Gleason all the way up to Ex-Mayor Jones, the previous season's BigBad, helped the gang with their plan in "Wrath of the Kampus".]]

--> [[spoiler: '''Sheriff Stone''': Can I play co-pilot? Because, well... I literally have no idea how to fly a helicopter.]]
--> [[spoiler: '''Mayor Nettles''': Sheriff, you can be ''my'' co-pilot ANYTIME.]]

--> [[spoiler: '''Daphne''': Where's Scooby going?]]
--> [[spoiler: '''Shaggy''': Where he goes every day, five times a day. [[ConversewiththeUnconscious To visit Nova]].]]

* Episode 48, "Nightmare In Red": [[spoiler: In the dream realm, Fred reconciles with Fred Jones Sr., or the "better side" of Fred Jones Sr. who admits to Fred that he's proud of him and that being his father was the best part of his life. Fred literally was the best part of him.]]
** [[spoiler: El Agguire breaks down sobbing, adamant that the Nibiru entity shouldn't be destroyed solely because the horrific acts he and his men have performed under its influence have damned them, and they deserve the punishment of being lost in the Sitting Room with no salvation. The Annunaki inhabiting Nova soothingly reassures him that, when Mystery Incorporated does defeat it, all of his misdeeds ''will'' be forgiven. It turns out to be because he will have never committed them.]]
* Episode 49, "Dark Night Of The Hunters": [[spoiler: Velma's heart-to-heart with her mother at the end and their hug. After her near-meltdown in episode 48, Velma needed that.]]
* Episode 50: [[spoiler:Fred comes right out and tells Daphne he loves her. It moves Daphne...and Velma...to tears.]]
** Also [[spoiler: Sheriff Stone comes out and tells Mayor Nettles that he loves her, also making an epic RousingSpeech to get the citizens of Crystal Cove to fight back at Pericles' robot forces.]]
** [[spoiler: Shaggy volunteers right away to start a prisoner uprising on the spot, then wonders what that weird feeling in his chest is. Scooby replies "Courage."]]
** [[spoiler: Daphne comforting Fred after he is forced to destroy the Mystery Machine.]]
--> [[spoiler: '''Fred:''' What have I done?]]
--> [[spoiler: '''Daphne:''' What you had to. What you always do. Turned traps into a fighting chance to live.]]
** [[spoiler: Even the villains get their share of heartwarming in this episode. Mr. E nostalgically looks into his own journal and wonders what happened to Cassidy, showing that he wasn't involved in her death and still deeply cared for her even after the curse. [[FreezeFrameBonus A look into the journal]] also shows that Pericles seemed to be jealous of Cassidy stealing Ricky's attention when she first met him (paralleling Scooby's jealousy of Shaggy and Velma), showing that the psychopathic bird once had a great deal of affection for his owner.]]
* [[spoiler: The Series Finale. Upon destroying the Nibiru Entity, it's erased from history, and everyone's lives turn for the better. Sheriff Stone and Mayor Nettles are married with four children, Fred's birth parents aren't psychotic and Daphne's parents now support her's and Fred's relationship, Shaggy is now an award winning chef, Ricky Owens owns a successful and environment friendly company, is thin, and married to Cassidy, and even Pericles isn't insane or evil.]]
** [[spoiler:Also, Fred Jones Sr. is a coach at Crystal Cove and considers Fred to be like a son to him, and Marcie is Velma's best friend, and the two have won dozens of academic awards together. The clincher about that last one? When Velma has a EurekaMoment about what has created this new timeline and rushes off to tell the Gang, Marcie simply smiles and says "That's my girl."]]
** [[spoiler:Before all that, the group realizing what the 'Heart of the Jaguar' ''really'' is: their [[ThePowerOfFriendship bond of friendship]]. They rally one another before rushing off to put down the Nibiru Entity once and for it together, as a team.]]
* [[spoiler: Nova, still under the control of the annunaki (presumably) watches Mystery Incorporated leave Crystal Cove one last time, and declares Scooby]] the bravest dog ever. Truly high praise from such a being who watched the gang [[spoiler: save the world.]]
** Even more so seeing as [[spoiler:the Annunaki are {{Time Abyss}}es,]] meaning if ''anyone'' can make that statement and it be NotHyperbole, it's [[spoiler:one of them.]]
* If one takes the [[spoiler:StealthPrequel aspect of the show and applies it as a prequel to the rest of the post-''Where Are You?'' canon, you get several of these.]]
** [[spoiler:90s-era movies that were sequels to ''Where Are You?'', then it means that Scooby was able to move on from Nova and found a SecondLove in [[WesternAnimation/ScoobyDooAndTheAlienInvaders Amber]].]]
** Fred is said to have become a mystery novelist after ''Where Are You?''. [[spoiler:Who's to say that he didn't write about the events of the show?]]
** Fred [[spoiler:choosing to continue going by "Fred Jones" rather than "Fred Chiles" in honor of his other father, though it's also a {{Tearjerker}} in that aspect for a few reasons.]]

-->'''Fred:''' There's a book over here... Daphne read a book once!
-->'''Fred:''' And this chair... Daphne liked to sit in chairs!

* In episode 12, despite constantly mocking H.P. Hatecraft and dissing his writing, Harlan Ellison shows up concerned for his safety when the monster kidnapped him. After Hatecraft is rescued and the bad guy caught, they have a NotSoDifferent moment when they realize they both have {{Loony Fan}}s, and Ellison proposes they co-write a book about said fans.

* Scooby apologizing to Velma for all the trouble he's caused in Velma and Shaggy's relationship.

* The end of episode 22 - a bit of a breather from all the dark stuff going on. Sheriff Stone even has fun!

* If one takes the [[spoiler:StealthPrequel aspect of the show and applies it as a prequel to the 90s-era movies that were sequels to ''Where Are You?'', then it means that Scooby was able to move on from Nova and found a SecondLove in [[WesternAnimation/ScoobyDooAndTheAlienInvaders Amber]].]]

* For the twists and turns and depression that was episode 26 [[spoiler: Mayor Jones]] rescuing Fred stood out for this troper and showed that even with all the abuse and neglect that he put him through, he still cared for Fred's safety.

** [[spoiler: Also, Fred Jones Sr. is a coach at Crystal Cove and considers Fred to be like a son to him, and Marcie is Velma's best friend, and the two have won dozens of academic awards together. The clincher about that last one? When Velma has a EurekaMoment about what has created this new timeline and rushes off to tell the Gang, Marcie simply smiles and says "That's my girl."]]

** [[spoiler: Even the villains get their share of heartwarming in this episode. Mr. E nostalgically looks into his own journal and wonders what happened to Cassidy, showing that he wasn't involved in her death and still deeply cared for her even after the curse. [[FreezeFrameBonus A look into the journal]] also shows that Pericles seemed to be jealous of Cassidy stealing Ricky's attention when she first met him (paralleling Scooby's jealousy of Fred and Velma), showing that the psychopathic bird once had a great deal of affection for his owner.]]

** [[spoiler: Even the villains get their share of heartwarming in this episode. Mr. E nostalgically looks into his own journal and wonders what happened to Cassidy, showing that he wasn't involved in her death and still deeply cared for her even after the curse. [[FreezeFrameBonus A look into the journal]] also shows that Pericles seemed to be jealous of Cassidy when she first met Ricky (paralleling Scooby), showing that the psychopathic bird once had a great deal of affection for his owner.]]

** Then, after [[spoiler: said man-crab does, in fact, capture Daphne]], Fred goes into a HeroicBSOD. He spends ''hours'' digging, [[CrowningMomentOfFunny wherever he is]], including in the Mystery Machine and Velma's room, [[spoiler: since she was dragged under the sand at the beach]], and then spends the next several minutes making random comments about Daphne.

* Given the amount of guest stars from previous Hanna-Barbera cartoons, this series could count itself as a [[CrowningMomentOfHEartwarming CMOH]], simply for the sheer amount of nostalgia it envokes. From Tom, Tub, Scooby, and Moby Dick, to Blue Falcon and Dynomutt the Dog Wonder, to Race Bannon and Dr. Benton Quest (with a nod to Bandit thrown into their dialogue), and even the guest stars of the DreamSequence episode (Jabberjaw, Speed Buggy, Captain Caveman, and the Funky Phantom), our favorite shows haven't been forgotten.

* [[spoiler: The Series Finale. Upon destroying the Nibiru Entity, it's erased from history, and everyone's lives turn for the better. Sheriff Stone and Mayor Nettles are married with four children, Fred's birth parents aren't psychotic and Daphne's parents now support her's and Fred's relationship, Shaggy is now an award winning chef, Ricky Owens owns a successful and environment friendly company, is thin, and married to Cassidy, and even Pericles isn't insane.]]

* Episode 48, "Nightmare In Red": [[spoiler: In the dream realm, Fred reconciles with Fred Jones Sr.]]
** [[spoiler: El Agguire breaks down sobbing, adamant that the Nibiru entity shouldn't be destroyed solely because the horrific acts he and his men have performed under its influence have damned them, and they deserve the punishment of being lost in the Sitting Room with no salvation. The Annunaki inhabiting Nova soothingly reassures him that, when Mystery Incorporated does defeat it, all of his misdeeds ''will'' be forgiven.]]

* The [[RomanticTwoGirlFriendship friendship between]] Velma and Hot Dog Water (Marcy) in Season 2 is made of heartwarming.

** [[spoiler: Also, Fred Jones Sr. is a coach at Crystal Cove and considers Fred to be like a son to him, and Marcy is Velma's best friend, and the two have won dozens of academic awards together. The clincher about that last one? When Velma has a EurekaMoment about what has created this new timeline and rushes off to tell the Gang, Marcy simply smiles and says "That's my girl."]]

** [[spoiler: Also, Fred Jones Sr. is a coach at Crystal Cove and considers Fred to be like a son to him, and Marcy is Velma's best friend, [[LesYay implied to be her girlfriend]], and the two have won dozens of academic awards together. The clincher about that last one? When Velma has a EurekaMoment about what has created this new timeline and rushes off to tell the Gang, Marcy simply smiles and says "That's my girl."]]

** Yeah he still cared for 'his' Fred's safety, but don't you think that [[FridgeHorror he might've needed him for something else?]]
** With the reveal from [[spoiler: Fred's real parents that Mayor Jones kept them away through threats of BODILY HARM to Fred, it's more likely than ever that this is a subversion of a heartwarming moment: if Fred got badly hurt or killed by accident, he'd have no more leverage and be exposed by Brad and Judy.]]

** [[spoiler: Also, Fred Jones Sr. is a coach at Crystal Cove and considers Fred to be like a son to him, and Marcy is Velma's best friend and the two have won dozens of academic awards together. The clincher about that last one? When Velma has a EurekaMoment about what has created this new timeline and rushes off to tell the Gang, Marcy simply smiles and says "That's my girl."]]

* [[spoiler: The Series Finale. Upon destroying the Nibiru Entity, it's erased from history, and everyone's lives turn for the better. Sheriff Stone and Mayor Nettles are married with four children, Fred's birth parents aren't psychotic and Daphne's parents now support her's and Fred's relationship, Shaggy is now an award winning chef, Ricky Owens owns a successful and environment friendly company, is thin, and married to Cassidy, and even Perricles isn't insane.]]