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Here it is people a listen of archenemies of characters in the Multi-Universe

The list

Megatron is the archenemy of the Disney Angels, the Autobots, and all who are free.

Slade (formerly) and Owlman (currently) is the archenemy of Dib.

The Powerpunk Girls to Bubbles and the Rowdyruff Boys

The Joker is Bender's primary and most recurring nemesis. While MOM, Terumi, Anarky and Discord were this to him as different points in his life and in the series. 

Eobard Thawne is set to be one to Rick, Bender, Skipper and Lydia 

The Master is the archenemy of the Doctor.

Hunson Abadeer, Dr. Weil,Ares, Ra's Al Ghul (Batman Begins) and Xerek are Lizbeth's main archenemies with the Coachman and Mechuckles being minor ones.

Hunson and Ra's Al Ghul for not so different reasons to Lizbeth

Xerek because Lizbeth saw through his harmless appearance and had him arrested while he fooled everyone else

Dr. Weil for giving Lizbeth so much shit in "The Multi-Universal War of Destiny", "Legends of Light and Darkness", and "Rise of Mechuckles: Beware of the Sith Stalker".

Baron Zemo to Phineas

Sebastain Shaw to Isabella an extent...Horace Black

Sektor to Frost

Dr. Blowhole (formerly) and Captain Chantel DuBois (currently) to Skipper

Iron Queen and Pretorius to Heloise. She shares the latter with Sam.

Ridley is this to Samus Aran.

Blackfire is the sister and archenemy of Starfire.

The Anti Fairies are this for Jorgen Von Strangle.

Negaduck is the archenemy of Darkwing Duck.

Snowball is the archenemy of Pinky and the Brain.

Hiroshi Sato is the father of and the archenemy of Asami.

Maximus I.Q for Atomic Betty

BlackGarurumon, Cooler, Sunset Shimmer, Sylar and Maximilian are the archenemies of Blue. He shares the first with Bender, the third and fifth with Twilight Sparkle, and the fourth with Riolu.

Dr. Doofenshmirtz (formerly) and Dr. Sam Isaacs (currently) is the archenemy of Perry the Platypus.

Quan Chi is the archenemy of Scorpion.

Darth Helmet and Lil' Gideon for Django Of The Dead.

Ganondorf is the archenemy of Link and Zelda.

Bowser is the archenemy of Mario and Luigi.

Xemnas is the archenemy of Sora, Donald and Goofy.

Zeus, Ares and Mechuckles are in the running for this to Maka Albarn. Zeus ends up being the main enemy.

Alec Trevalyn for Stan Smith.

Frieza, Cell, Kid Buu, and Omega Shenron are the archenemies of Goku, Vegeta and the Z Fighters.

Meltdown was this to Sari Sumdac before his death, before she herself became this for Jack Frost.

Cecliate is the archenemy of Johnathan Tangelo and WingVeemon.

Rydak is the father and archenemy of Landarick.

Duskmon is the archenemy of Terra, Riolu and Patch.

M. Bison is this to Sagat and Chun-Li.

Mesogog is the archenemy of Buddy.

Makuta Teridax and King Sombra are the archenemies of Takua.

Dr. Nefarius and Aldrich Killian are the archenemies of Ratchet and Clank.

Falcon is the archenemy of Stuart and Margalo.

Jaba the Hutt and Cain (Robocop) are the archenemies of Han Solo.

Vaati (until his death) and William Birkin (currently) is the archenemy of Gilbert.

Bertram Griffin to Stewie Griffin.

Malefor is the archenemy of Spyro.

Niju and Galacta Knight are the archenemies of Aleu.

Pitch and Sari Sumac are the archenemies of Jack Frost.

Keenan is archenemy of Buddy, Shiny and Don.

Giovanni is the archenemy of Ash, Pikachu, Green and Silver.

Nightmare is the archenemy of Meta Knight and Kirby.

Blackbeard and Davy Jones are the archenemies of Jack Sparrow.

Maxim Horvath is the archenemy of Balthazar Blake.

Evanora is the archenemy of Sabrina Spellman.

Rico Dredd is the brother and archenemy of Judge Dredd in addition to Scamp and Angel.

Goth is the archenemy of Shade and Marina.

Turbo is the archenemy of Ralph, Vanellope and Felix.

Dr. Wily is this for Megaman.

Firelord Ozai is the archenemy of Aang, Katara and Zuko.

Shao Kahn is the archenemy of Raiden (Mortal Kombat).

Shang Tsung is the archenemy of Liu Kang.

Mileena is the archenemy of Kitana and Jade.

Kano is the archenemy of Sonya Blade.

Sauron is the archenemy of Frodo.

Scorch is the archenemy of Winger.

Ares (DC) is the archenemy of Wonder Woman (until her death), Death the Kid and Makoto.

Sephiroth is the archenemy of Cloud.

Vector is the archenemy of Gru.

Grigori Rasputin is the archenemy of Hellboy.

The Huntsman and Dark Dragon are the archenemies of Jake Long.

Steele is the archenemy of Balto and Kodi.

Djinn is the archenemy of Genie.

Dracula (Castlevania) is the archenemy of Alucard, Maria and the Belmont clan.

Shere Khan is the archenemy of humans since he hates man.

Sigma to X and Zero

Grings Kodai is the archenemy of Zorua.

Darkseid is the father and archenemy of Orion.

Mechakara to Linkara

The Entity/MissingNO is this to Angry Video Game Nerd and Lord Vyce

Peter Pan towards his son, Mr. Gold

The Kousuke Kira is Romeo Conbolt's primary and most recurring nemesis. While Pandora, Hades, and Dr. Fetus were this to him as different points in his life and in the series.