Storylines
Below are links to the beginning of each storyarc in the comic

 

Super Smash Bros. Melee

The Legend of Zelda

Super Mario Bros.

The Legend of Zelda 2: The Adventure of Link

R.C. Pro-AM

Megaman

Metroid

Super Mario Bros. 2

EarthBound

Super Mario Sunshine

Comic Poisoning

The Legend of Zelda: The Wind Waker

Megaman X2

100th Comic

Pong

Q*Bert

Pac-Man

Pitfall

Hylian History

Mario is Missing

Luigi's Mansion

The Light World Meets the Dark World

Sonic the Hedgehog

Megaman 2

One Year Comic

Metroid Prime

Kirby's Adventure

Super Mario 64

The Matrix

Sonic the Hedgehog 2

Megaman 3

The Legend of Zelda: Link to the Past

Breaking into the Hidden Room

200th Comic

3D Chao

Sonic the Hedgehog 3 and Knuckles

Donkey Kong

Megaman 4

Tetris

Sonic CD

Super Mario Bros. 3

Mario Kart Series

Two Year Comic

Megaman 5

Game Over Scrolls

Knuckles Chaotix

Super Mario World

Megaman 6

Sonic 3D Blast

The End of an Era

The Legend of Zelda: Link's Awakening

Super Mario Land

Metroid 2: The Return of Samus

SSBM Final Fight

Super Mario RPG

Metroid Prime 2: Echoes

300th Comic

Pikmin 2

The Legend of Zelda: Minish Cap

Three Year Comic

Sonic Adventure

The Legend of Zelda: Ocarina of Time

Paper Mario

Paper Mario 2

Assassin's Creed

Kid Icarus

Sonic Adventure 2

Zero Wing

Megaman 7

Mario and Luigi: Superstar Saga

Sonic Heroes

The Alien Alliance

The Legend of Zelda: Twilight Princess

Kirby 64: The Crystal Shards

Mario and Luigi: Partners in Time

Shadow the Hedgehog

Portal

Super Mario Galaxy

Metal Gear

Dead Rising

Overlord

Metroid Prime 3: Corruption

Sonic and the Secret Ring

Super Paper Mario

Shadow of the Colossus

Super Metroid

Megaman 9