What you see before you is a list of story ideas in that order with a description. Takes place after "ROTTMNT: Many Unhappy Returns" and during S1 - S2 of DCSHG. This is all I can come up with so far, but if you guys have any ideas you like to share feel free to comment.
1. #MutantsInMetropolis: Mutants started appearing in the city of Metropolis along with four new heroes.
2. #TheCritterGang: With the girls help, the turtles found themselves a new hideout in Metropolis. But their hideout gets overrun by mutant raccoons.
3. #AllYouCanEatSuperBuffet: Berry and other meta humans have gone missing. (Featuring the Invinci-Bros, Super Villain Girls and Meat Sweats)
4. #DancingWithTheDevil: An out-of-control mutant Tasmanian devil wreaks havoc in Metropolis just by dancing.
5. #FirstDayOfSchool: The turtles disguise themselves as humans to get into school in order to capture some of the Oozesquitoes inside. (Featuring April O'Neil and Mutagen Man)
6. #Spike: Raph stumbles upon a baby alien lizard and keeps it as a pet.
7. #TurtlesOnTheJob: Now that the turtles can blend in with humans properly, they decided to apply for part-time jobs and earn some coinage. (Featuring Ice Cream Kitty)
8. #LivingTheNightmare (M+H Edition): When the turtles are held captive in their nightmares by demon dream beavers, the Superhero Girls will have to confront their own hidden insecurities, or risk the Teenage Mutant Ninja Turtles being trapped in a prison of their own fears forever.
9. #ArchNemesis: Warren Stone comes to Metropolis to find himself a new arch nemesis and has chosen Supergirl.
10. #LeaderSwap: After failing to apprehend a mutant skunk criminal, Raph and Wonder Woman argued about each other's leadership. To prove who's the better leader and see how both teams work, Diana and Raph swap teams for a day. (Featuring the Master of Games)
11. #ScarmbledEggs (M+H Edition): The heroes and villains are given a home economics class assignment where they are paired up with another student and given an egg to care for over a weekend.
12. #SuperDuperPets: The Superhero Girls' pets got mutated by the Oozesquitoes. (Featuring Superdog, Bat-Hound, Dex-Starr, Goldberg, Merlin, and Harry Houdini)
13. #TeaTimeWithZoe: Raph has been having secret playdates with a little girl named Zoe Lawton. (featuring Mrs. Cuddles, Toyman, and Deadshot)
14. #ToxicAlliance: After Poison Ivy encounters Baron Draxum, she discovers a new power and gets the turtles to be her first mindless slaves.
15. #Raph'sLoveStory: Karen asked Raph to hang out. Just the two of them... alone. (RaphxKaren Chapter)
16. #Nano: Donnie and Barbara discover a swarm of nanobots that think of them as their parents.
17. #VillainTeam-Up: Foot Recruit wants revenge on the turtles for stopping the shredder, so she teams up with the Supervillain Girls to get back at them.
18. #DramaQueen (M+H Edition): Leo gets the starring role in Zee's school play, but someone is trying to sabotage the play. Leo thinks it's Oliver Queen.
19. #TheExterminator: A mutant cyborg cockroach is after Supergirl.
20. #MutantsInNeed: Mikey and Jessica see friendly mutants being mistreated by humans. They work together to make people see that not all mutants are bad. (Leatherhead, Mondo Gecko, Ray Fillet, and Scum Bug)
21. #BreakingNews (M+H Edition): Lois Lane's attempt to get an internship at the Daily Planet leads to her trying to unmask the Teenage Mutant Ninja Turtles, April and Hal work together to keep the turtles' identity a secret.
22. #SliverSentry: Kara's long-lost friend from Krypton, Jes Synn-Vaz, is on the run from a space bounty hunter named Lobo.
23. #SnakeInTheGrass: Mikey was bitten by a mutant snake and the team must get the antidote before time runs out. (Featuring Copperhead and MikeyxJessica Chapter)
24. #SuperMon-star: Zee and Leo get to perform a play at the Metropolis Theatre. However, Zee seems to have trouble acting with Leo. Meanwhile, a clay-like monster is wreaking havoc all over Metropolis. (Featuring Clayface and LeoxZee Chapter)
25. #AmBatgirl (M+H Edition): Batgirl finally has the chance to live out her life's dream and be the sidekick to her hero and inspiration - the Batman (Featuring Deathstroke and DonniexBarbara Chapter)
26. #GoingBackHome?: The heroes have captured all of the Oozesquitoes in Metropolis. Now the turtles will have to say goodbye to their new friends. (featuring Master Splinter and Todd)
27. #TheAquamanCometh (M+H Edition): For months, Garth sends Aquaman letters that greatly exaggerate his accomplishments in Metropolis; when the King of Atlantis comes for a surprise visit, Garth begs the Super Hero Girls to help cover for his little white lies.
28. #MutantBrawl: Raph and Splinter meet a spunky blonde girl named Dinah Lance and discover a secret fight club involving human and mutant competitors. (Featuring Black Canary, Wildcat, Bebop, Rocksteady, Killer Croc, Bane and Roulette)
29. #ThatNightAtAlbeartos: Donnie, Diana and Harleen are stuck inside a newly opened Albeartos in Metropolis at night.
30. #BrainAndBrawnVerusBiggerBrain: Supergirl and Silver Sentry work together to stop a mutant albino gorilla. (Featuring Ultra Humanite)
31. #NightmareInGotham (M+H Edition): Babs and Harleen bring the girls and the turtles to Gotham City to celebrate Halloween! However, the fun is put on hold when the heroes run into Gotham's most notorious Super Villain. (Featuring Scarecrow)
32. #InnerDemons: Sometime after their battle with the Joker, the turtles grow concerned about their new dark power. (The sword of Tengu. The tonfās of Red Oni. The kunsari-fundo of Kitsune. The crystal of Baku.)
33. #Armaggon: An unexpected team-up of Aqualad and Livewire when they work together to stop a mutant shark from taking all the power in Metropolis and use it to take over Atlantis.
34. #ComicConWrong: Donnie, Barbara, Leo, and Garth are at a comic convention where they meet a comic book artist whose drawings come to life.
35. #TheFreshPrincessOfReinFaire (M+H Edition): Ember has princess on the menu. Can the heroes outwit the dragon before Ember claims her princess?
36. #GoForItKara!: Mikey and Karen help Kara ask Jes Synn-Vaz to be her Valentine. (Featuring Mongul)
37. #TheEnchantingCirce: While everyone is getting ready for the big dance at Metropolis High, Diana's longtime enemy shows up.
38. #PlanetOfTheMutants: Lex Luthor plans on turning all the Humans in the entire world into mutants. (Man-Bat, Leatherhead, Copperhead, Ultra Humanite, Mutagen Man, Armaggon, Orca, The Critter Gang)
39. #SummerInNewYork: With Summer here and Lex Luthor defeated, the heroes decided to take it easy at the Big Apple.
40. #TheLairGames (M+H Edition): April presents her award-winning documentary about the Turtles' annual event: The Lair Games.
41. #Ananda'sRevenge: An old superhero named Dr. Dome has gone rogue and started capturing veteran members of the Justice Force. (Stainless Steel Steve, Joey Lastic, Zippy Lad, Superman, Batman, Elongated Man, Flash, and the Exterminator)
42. #RepairinTheBaron (M+H Edition): Mikey embarks on his craziest mission: trying to get Baron Draxum to tolerate humans.
43. #NanoReturns: The surviving nanobots were discovered by the Critter Gang. In their attempts to hack it, the Critter Gang caused Nano to malfunction and go berserk.
44. #PizzaPuffs (M+H Edition): Raph's brothers and Diana's friends accidentally eat pizza puffs laced with a mystic toxin.
45. #I'mNobody: April and Batgirl meet a masked female vigilante who has a personal vendetta with a gang of street thugs, The Purple Dragons. (Featuring Hun)
46. #TalesOfTheHiddenCity (M+H Edition): the heroes split up into groups to do their own thing in the hidden city.
47. #TheButterflyAndTheFish: Two Yokai gladiators escaped from the Battle Nexus. (Featuring Tsunami, Chrysalis, and Oni)
48. #ClothesDon'take the turtle (M+H Edition): Hypno-Potamus traps the turtles and the girls in a magical 80s movie montage.
49. #BirdsOfPrey: Huginn and Muninn befriend a headstrong kid named Tyler, on the run from a gang of mobsters. (Featuring Harley Quinn, Poison Ivy, Livewire, Black Canary, Katanna, Leatherhead and Walrus)
50. #FistOfFury (M+H Edition): April and the girls must help Splinter save his chain of dojos from being taken over by an evil rival.
51. #BattleNexusNewYork (M+H Edition): Big Mama turns New York City into her new Battle Nexus arena and the TMNT have to fight to save everyone they love.
52. #GrandFinale: the TMNT and the Superhero Girls are about to face their most powerful and deadliest foe yet, the Shredder.
53. #HeroesInTime: Leo finds an ancient times relic that accidentally sends him, his brothers, and the girls through space and time.
54. #Mutants+HeroinesTheMovie: The TMNT and the Superhero Girls are put to the ultimate test when ruthless creatures from another universe look to unleash extreme chaos. (Featuring Martian Manhunter)