List of Bosses

I can't think of a story

Mushroom Kingdom

 * Boom Boom & Pom Pom
 * Popple
 * Tatanga
 * End Boss: Petey Piranha

Subcon

 * Reznor
 * Birdo
 * Mouser
 * End Boss: Wart

Smithy's Dimension

 * Larry Koopa
 * Goomboss
 * Whomp King
 * Megaleg
 * King Bob-omb
 * End Boss: Smithy

Beanbean Kingdom

 * Morton Koopa Jr.
 * Mario
 * Queen Bean
 * End Boss: Cackletta

Palace of Shadow

 * Wendy O. Koopa
 * Sir Grodus
 * Bonetail
 * End Boss: Shadow Queen

Blooper Beach

 * Iggy Koopa
 * Unagi the Eel
 * Kingfin
 * End Boss: Gooper Blooper

Shroob Kingdom

 * Roy Koopa
 * General Guy
 * Princess Shroob
 * End Boss: Elder Princess Shroob

Poisoned Swamp

 * Lemmy Koopa
 * Giant-Sized Wiggler
 * Wario & Waluigi
 * End Boss: Donkey Kong

Castle Bleck

 * Ludwig von Koopa
 * O'Chunks
 * Mimi
 * Mr. L
 * Count Bleck
 * End Boss: Dimentio

Boo's Woods

 * Mad Piano
 * Bouldergeist
 * Dry Bowser
 * End Boss: King Boo

Peach's Castle

 * Midbus
 * Fawful
 * Kamek & Kammy Koopa
 * End Boss: Dark Star

Dream World

 * Grobot
 * Zeekeeper
 * Bowser Jr.
 * End Boss: Antasma

Bowser's Castle

 * Army Hammer Bro.
 * End Boss: Bowser

Subspace

 * Master Hand
 * Crazy Hand
 * Master Core
 * End Boss: Tabuu

Gravity Falls Entrance

 * Manly Dan
 * Wendy Corduroy
 * Mabel Pines
 * End Boss: Dipper Pines

Gravity Falls Stage 1

 * Pa & Ma Duskerton
 * End Boss: Robbie Valentino & Tambry

Northwest Manor

 * Pacifica Northwest
 * End Boss: Preston Northwest

Gravity Falls Stage 2

 * Old Man McGucket
 * End Boss: Blind Ivan

Forest

 * Gnome Monster
 * Gremloblin
 * The Hide-Behind
 * End Boss: Shape Shifter

Man Caves

 * Chutzpar
 * Leaderaur
 * Multi-Bear
 * End Boss: Pterodactyl

Arcade

 * Rumble McSkirmish
 * Phantom Foxy
 * Phantom Balloon Boy
 * Phantom Chica
 * Giffany
 * Phantom Freddy
 * Phantom Puppet
 * End Boss: The Killer

Future City

 * Kurt Zisa
 * Lolph & Dundgren
 * Blendin Blandin
 * End Boss: Time Baby

Deep Forest

 * The Beast
 * End Boss: Summerween Trickster

Gravity Falls Prison

 * Sheriff Blubs & Deputy Durland
 * End Boss: Gideon Gleeful

Gravity Falls Stage 3

 * Unnamed Dispatcher
 * End Boss: Agents Powers & Trigger

Mystery Shack

 * Soos Ramirez
 * End Boss: Stan Pines

The Apocalypse

 * Stanley Pines
 * End Boss: Bill Cipher

South Park Stage 1

 * Bebe Stevens
 * Trent Boyett
 * Stan Marsh
 * End Boss: Kyle Broflovski

South Park Elementary

 * Kenny McCormick
 * Butters Stotch
 * Wendy Testaburger
 * End Boss: Eric Cartman

South Park Stage 2

 * Shelly Marsh
 * Randy Marsh
 * General Disarray
 * End Boss: Professor Chaos

Clyde's House

 * Craig Tucker
 * End Boss: Clyde Donovan

Chili Con Carnival

 * Tuong Lu Kim
 * End Boss: Scott Tenorman

Caverns

 * Gnome Warlock
 * End Boss: Crab King

Forest

 * Al Gore
 * Reptilian Bird
 * Queen Spider
 * End Boss: Manbearpig

South Park Stage 3

 * Sheila Broflovski
 * Detective Harrison Yates
 * Tom Cruise
 * End Boss: Mecha-Streisand

Super Adventure Club

 * Darth Chef
 * End Boss: William P. Connelly

Heaven

 * Muhammad
 * Jesus
 * God
 * End Boss: Saddam Hussein

Hell

 * Damien Thorn
 * Anti-Christ
 * Beelzaboot
 * End Boss: Satan

Peru

 * Tooth Decay
 * End Boss: Micheal Chertoff

Gulf of Mexico

 * Jim McElroy
 * End Boss: Cthulhu

South Park Stage 4

 * End Boss: Big Bad Government Guy

Tree Fort

 * Jake the Dog
 * End Boss: Finn Mertens

Grasslands Stage 1

 * Billy
 * Demon Cat
 * Fear Feaster
 * End Boss: Magic Man

Grasslands Stage 2

 * Evil Monster
 * King Worm
 * Darren
 * End Boss: Maja

Candy Kingdom

 * Gumball Guardians
 * Ricardio
 * Lady Rainicorn
 * End Boss: Princess Bonnibel Bubblegum

Bad Lands

 * Xergiok
 * The Beast
 * Death
 * End Boss: Lemongrab

Red Rock Pass

 * Marauder Leader
 * End Boss: Marceline Abadeer

Ice Kingdom

 * Gunter
 * End Boss: Ice King

Fire Kingdom

 * Flame Princess
 * End Boss: Flame King

Lumpy Space

 * End Boss: Lumpy Space Princess

The Pit

 * End Boss: Kee-Oth

Land of Aaa

 * Cake the Cat
 * Fionna Mertens
 * Marshall Lee
 * End Boss: Ice Queen

Wizard City

 * Grand Master Wizard
 * End Boss: Bella Noche

Nightosphere

 * End Boss: Hunson Abadeer

Multiverse

 * Cosmic Owl
 * Prismo
 * Martin
 * End Boss: The Lich

Park Entrance

 * Rigby
 * End Boss: Mordecai

Park Path

 * Pops Maellard
 * Mitch Sorenstein & High-Five Ghost
 * Skips
 * End Boss: Benson

The Park Stage 1

 * The Urge
 * Susan
 * Lemon Chef
 * End Boss: Destroyer of Worlds

Park Outskirts

 * Baby Ducks
 * The Sheriff
 * Ybgir
 * End Boss: Death Bear

The City

 * Eileen Roberts
 * Starla Gutsmandottir
 * Margaret Smith
 * End Boss: Cloudy Jane

The Park Stage 2

 * Moon Monster
 * Warlock
 * Guardian of Secrets
 * End Boss: Goose Monster

The House

 * Stealth Co. Guy
 * The Blue Thing
 * Jan the Wallpaper Man
 * End Boss: Jebediah Townhouse

Graveyard

 * Howard Fightington
 * Scarecrow
 * Spirit of the Harvest Moon
 * End Boss: Halloween Wizard

Death’s House

 * King Ramses
 * End Boss: Death

The Park Stage 3

 * Nicolai
 * End Boss: Hammer

Eastern Pines

 * Stag-Man
 * Mitsuru Shinehara
 * Gene
 * Richard Buckner
 * Snowballs the Ice Monster
 * End Boss: Quillgin

Techzone

 * Limosaurus
 * Doom Ma Geddon
 * VC-Arbitrator
 * End Boss: Internet

Guardians’ Lair

 * Reginald
 * End Boss: Klorgbane the Destroyer

Exit 9B

 * Garrett Bobby Ferguson Jr.
 * End Boss: Garrett Bobby Ferguson

Ponyville Stage 1

 * Lyra Heartstrings & Sweetie Drops
 * Scootaloo
 * Sweetie Belle
 * Apple Bloom
 * Scootie Belloom (Fusion of the CMC)
 * End Boss: Diamond Tiara

Castle of the 2 Sisters

 * Headless Horse
 * Lightning Dust
 * Pony of Shadows
 * Nightmare Rarity
 * Shadowfright
 * End Boss: Nightmare Moon

Ponyville Stage 2

 * Zecora
 * Gilda
 * Cheese Sandwich
 * DJ Pon-3 & Octavia Melody
 * Ursa Minor
 * End Boss: Trixie Lulamoon

Everfree Forest

 * Tatzlwurm
 * Well-to-Do
 * King Aspen
 * Cragadile
 * Squirk the Sea Emperor
 * Ursa Major
 * Ampelos
 * End Boss: Discord

Appleloosa

 * Chief Thunderhooves
 * Sheriff Silverstar
 * Jim the Cave Troll
 * Giant Tarantula
 * Chimera
 * Daring Do
 * Chupacabra
 * End Boss: Ahuizotl

Ponyville Stage 3

 * Timberwolf King
 * Flutterbat
 * Mare Do Well
 * Maud Pie
 * Dr. Whooves & Derpy Hooves
 * End Boss: Flim & Flam

Cloudsdale

 * Aria Blaze
 * Mothman
 * Sonata Dusk
 * Spitfire
 * Arabus the Windking
 * Sunset Shimmer
 * Adagio Dazzle
 * End Boss: Midnight Sparkle

Manehattan

 * Coco Pommel
 * Suri Polomare
 * Hoofbeard & Jewel
 * Chief Stablemaker
 * Rough Diamond
 * End Boss: Mane-iac Mayhem

Canterlot

 * Hydra
 * Princess Luna
 * Shining Armor
 * Lavan the Firelord
 * Princess Celestia
 * End Boss: Queen Chrysalis

Equal Town

 * Princess Trixie
 * Duchess Chrysalis
 * Captain Goodguy
 * Mirror Sombra
 * Mirror Celestia & Mirror Luna
 * End Boss: Starlight Glimmer

Crystal Empire

 * Kraken
 * Cerberus
 * Spike
 * Flash Sentry
 * Princess Cadence
 * End Boss: King Sombra

Tartarus

 * Smooze (King Mook of the Smoozelings)
 * Empreror Grogar
 * Scorpan
 * End Boss: Lord Tirek

Friendship Rainbow Kingdom

 * Applejack
 * Rainbow Dash
 * Rarity
 * Princess Disharmony (Fusion of Adagio Dazzle, Sonata Dusk, Aria Blaze, Suri Polomare, Lightning Dust, Trixie & Gilda)
 * Fluttershy
 * Pinkie Pie
 * Princess Twilight Sparkle
 * End Boss: Princess Harmony (Fusion of Twilight Sparkle, Pinkie Pie, Fluttershy, Rarity, Rainbow Dash, Applejack & Sunset Shimmer)

Equestrian Ruins

 * Meghan McCarthy
 * Fausticorn
 * Windigo King
 * End Boss: Star Swirl the Bearded

Elmore Stage 1

 * Anais Watterson
 * William
 * Rocky Robinson
 * Jamie
 * Margaret Robinson
 * End Boss: Gaylord Robinson

Elmore Junior High

 * Banana Joe
 * Razor
 * Principal Nigel Brown
 * End Boss: Miss Lucy Simian

Elmore Stage 2

 * Virus
 * Ant-One
 * Granny Jojo
 * End Boss: Nicole Watterson

Warped Elmore

 * Masami
 * End Boss: Richard Watterson

Elmore Park

 * Harold Wilson
 * Jackie Wilson
 * Tobias Wilson
 * End Boss: Tina Rex

Dream Elmore

 * Jealousy
 * End Boss: Zach

Downtown Elmore

 * Doughnut Cop
 * The Sheriff
 * Orange Woman
 * End Boss: Sal Left Thumb

Chanax, Inc

 * Chimera
 * The Internet
 * Goblin
 * End Boss: Mr. Chanax

Elmore Stage 3

 * Carlton & Troy
 * Darwin Watterson
 * Kenneth
 * End Boss: Hector Jotunheim

Elmore Cemetery

 * Carrie Krueger
 * The Snatcher
 * Dark Gumball
 * End Boss: Anderous

Elmore Stage 4

 * The Eggheads
 * Clayton
 * Ocho
 * End Boss: Bobert

Forest of Doom

 * Mrs. Fitzgerald
 * Moose-Like Creature
 * Jeff the Killer
 * Patrick Fitzgerald
 * Slender Man
 * End Boss: Penny Fitzgerald

Elmore in Ruins

 * End Boss: Gumball Watterson

The Void

 * Rob


 * End Boss: Maximus Vice

Los Angeles

 * Tracks
 * Cliffjumper
 * Blaster
 * End Boss: Jazz

London

 * Gnaw
 * The Dweller
 * Quintesson Judge
 * End Boss: Alpha Quintesson

Berlin

 * Wheelie
 * Chromia
 * Blurr
 * End Boss: Bumblebee

Washington D.C.

 * Ratbat
 * Frenzy
 * Rumble
 * Ravage
 * Laserbeak
 * End Boss: Soundwave

Tokyo

 * Wreck-Gar
 * Springer
 * Prowl
 * Kup
 * Sentinel Prime
 * End Boss: Metroplex

Chicago

 * Devastator
 * Hardshell
 * Dr. Arkeville
 * Kickback
 * Sharpshot
 * Nemesis Prime
 * The Driller
 * End Boss: Shockwave

Amazon

 * Sludge
 * Wheeljack
 * Swoop
 * Hound
 * Slug
 * Perceptor
 * Snarl
 * End Boss: Grimlock

Mars

 * Flamewar
 * Blitzwing
 * Lugnut
 * Straxus
 * Astrotrain
 * End Boss: Trypticon

The Moon

 * Autobot X
 * Drift
 * Elita One
 * Jetfire
 * Alpha Trion
 * End Boss: Omega Supreme

Kennedy Space Center

 * Old Snake
 * Slipstream
 * Menasor
 * Skywarp
 * Thundercracker
 * End Boss: Starscream

Autobot City

 * Mirage
 * Sky Lynx
 * Ratchet
 * Superion
 * Arcee
 * End Boss: Ironhide

Decepticon Base

 * Bludgeon
 * Bruticus
 * Lockdown
 * End Boss: Megatron

Autobot Base

 * Windblade
 * Defensor
 * Ultra Magnus
 * End Boss: Optimus Prime

Cybertron

 * Scourge
 * Cyclonus
 * Necrotitan
 * Galvatron
 * Thunderwing
 * End Boss: Unicron