Below is a list of locations and the character you will find there when you have completed Story mode.

Liquid: In front of ruins (before event)
Okita: In front of ruins (before event)
Check: Inside testing room
Nino: Inside testing room
Sayer: Inside testing room (far left)

Tashiro: Left side
Smith: Right side
Lazar: In front of gate

Torunka: Main Square
Eiki: Zeman's Castle
Zape: Zeman's Castle
Regulus: East of Main Square
Key Mace: Main Square
Key Mace #2: East of Main Square
Gate Mace: Outside Town, behind tree in area where you first arrive

Kalin: Enforcers Hideout
Trudge: Entrance Area
Itsuki: Entrance Area
Annie: Entrance Area
Arashiyama: Team Black & Blue's Hideout, left side of 1st floor
Clock: Team Black & Blue's Hideout, middle of 2nd floor
Kiyoto: Team Black & Blue's Hideout, far right of 3rd floor
Hiroyuki: Outside Team Black & Blue's Hideout
Natsumi: Outside Team Black & Blue's Hideout (must rescue Hana first)
Kuroe: Team Dirty Works Hideout
Kameno: Team Dirty Works Hideout
Ida: Team Dirty Works Hideout
Hayakawa: Outside Team Dirty Works Hideout
Gordon: Outside Team Dirty Works Hideout
Narumi: Card Shop
Salida Noula: Card Shop
Yusuke: Card Shop
Mimi: Outside Card Shop
Chihiro: Outside Card Shop
Sumetana: In front of Securities building

Facility Chief: Facility (must have examined flier near Peko)
Blister: Blister's Room
Bolt: Blister's Room
Dexter: Underground Duel Arena
Liquid: Spare Room (after event)
Okita: Spare Room (after event)
Jean: Outside Bootleg
Robinson: Outside Bootleg
Coppola: Inside Bootleg
Angie: Underground Duel Arena Entrance
Morrison: Underground Duel Arena Entrance
Figaro: Underground Duel Arena
Corse: Underground Duel Arena (must have Akiza as Tag Partner)
Aase: Entrance Area
Oscar: Parts Shop
Kalisse Noula: Parts Shop
Kawasaki: Parts Shop
Motoi: Outside Parts Shop
Fukoka: Outside Parts Shop
Grammy: Card Shop
Alina Noula: Card Shop
Roy: Card Shop
Ticera: Outside Card Shop
Honda: Outside Card Shop
Peko: Structure Deck Duels

Crow: Old Highway
Yusei: Old Highway
Igusa: Team Non-Securities Hideout, outside
Hashinoshima: Team Non-Securities Hideout, outside
Torino: Team Non-Securities Hideout, inside
Mitchie: Team Non-Securities Hideout, inside
Gushizawa: Team Non-Securities Hideout, roof
Tetsuzo: Entrance Area
Sugimoto: Entrance Area
Globe: Parts Shop
Lagoon Noula: Parts Shop
Rossi: Parts Shop
Roy: Outside Parts Shop
Oda: Outside Parts Shop
Anna: Outside Parts Shop
Hideki: Old Highway

Akiza: Highway
Leo: Entrance Area
Luna: Entrance Area
Jack: Duel Stadium - Outside
Hunter: Duel Stadium - Outside
MC: Duel Stadium - Inside
Randsborg: Duel Stadium - Inside
Carly: Waiting Room
Mina: Waiting Room
VP Heitmann: Lower left corner of Entrance Area
Seria: West of Entrance Area
Giado: West of Entrance Area
Kurihara: Stadium Gates
Shirase: Stadium Gates
Bass: Highway

When you complete Story mode you will be able to purchase Giganto L (Kalins duel runner) for 40 star chips from Chihiro.

When you complete Story mode the 'New Game (Existing Data)' option will become available. In this feature you can replay the 5d's Story mode with ALL previously collected cards and the same World Championship progress.

Complete the following tasks to get the corresponding item of clothing.

Unlock Career Suit:
Box item in the southwest room of the Securities building.

Unlock Dark Magician Girl:
Defeat Grammy seven times as a female character.

Unlock Dark Singer:
Complete Story mode, then purchase for 15 Star Chips from Chihiro.

Unlock Denim Jacket:
Purchase for 5 Star Chips from Chihiro if male.

Unlock The Enforcers:
Available at the start of Chapter 2.

Unlock One-piece:
Purchase for 5 Star Chips from Chihiro if female.

Unlock Race Queen:
Purchase for 5 Star Chips from Chihiro if female.

Unlock Rock N' Roller:
Box item inside the third duel gang's hideout if male.

Unlock Rough Style:
Box item in the basement of the first duel gang's hideout

Unlock Sailor Uniform:
Box item inside Zeman's castle if female.

Unlock Security Uniform:
Recieved from Crow in Chapter 2.

Unlock Stuffed Collar Uniform:
Box item inside Zeman's castle if male.

Unlock Tag Force Set:
Get 100% card completion.

Unlock Wild Style:
Purchase for 5 Star Chips from Chihiro if male.

Unlock Worn-out Clothes:
Box item inside the third duel gang's hideout if female.

Unlock Yusei Jacket:
Defeat Yusei ten times in Turbo Duels.

When you have completed the following tasks the corresponding opponent tag teams in World Championship mode will become available. Unlisted teams are either already available or become available through progress in Story mode.

Unlock Child of Chaos:
Complete Team 'Water & Fire' 3 times.

Unlock Cyber Regeneration:
Complete Team 'Angels & The Fallen' 3 times.

Unlock Dragon & Dragon:
Summon Five-Headed Dragon.

Unlock Dual Duel:
Complete Team 'Removal Guys' 3 times.

Unlock Duel Ritual:
Complete 300 Single Duels.

Unlock E & D Impact:
Complete Team 'Darkness + Fiends' 3 times.

Unlock Earthbound Crystal:
Summon Rainbow Dragon.

Unlock Fish-the-World:
Have 200 Spells and Traps activated.

Unlock Gadget Emperor:
Complete 150 Tag Duels.

Unlock Grinder Summoning:
Complete Team 'Explosive Tag' 3 times.

Unlock Legend's Anniversary:
Complete Team 'Love Reptiles?' 3 times.

Unlock Lo and Behold:
Complete Team 'Protect & Burn' 3 times.

Unlock Mausoleum's Legend:
Complete Team 'Order in Chaos' 3 times.

Unlock Simochi Study:
Complete Team 'Cyber Dragunity' 3 times.

Unlock Storm of Darkness:
Complete Team 'Fusion & Synchro' 3 times.

Unlock To the Graveyard:
Complete 75 Turbo Duels.

Unlock Trago Genex:
Summon VWXYZ - Dragon Catapult Cannon.

Unlock Zombie Path:
Win by attacking with Skull Servant.

When you have completed the following tasks the corresponding opponent will become available in World Championship mode. Unlisted opponents are either already available or become available through progress in Story mode.

Unlock Ancient Gear Gadjiltron Dragon:
Summon Ancient Gear Gadjiltron Dragon.

Unlock Archlord Kristya:
Complete 'Green Baboon, Defender of the Forest' 3 times.

Unlock Blackwing - Vayu the Emblem of Honor:
Summon Blackwing - Silverwind the Ascendant.

Unlock Blue-Eyes White Dragon:
Complete 'Darklord Desire' 3 times.

Unlock Chaos Sorcerer:
Complete 'Solar Flare Dragon' 3 times.

Unlock Crusader of Endymion:
Activate Mega Ton Magical Cannon.

Unlock Cyber Eltanin:
Complete 'B.E.S. Big Core MK-2' 3 times.

Unlock Dark Simorgh:
Complete 'Great Shogun Shien' 3 times.

Unlock Darkness Neosphere:
Play for 100 hours.

Unlock Destiny End Dragoon:
Complete 'Underground Arachnid' 3 times.

Unlock Dragunity Knight - Gadearg:
Complete 'Ancient Fairy Dragon' 3 times.

Unlock Earthbound Immortal Wiraqocha Rasca:
Win with by using the effect of Final Countdown.

Unlock Elemental Hero Absolute Zero:
Complete 'Fabled Leviathan' 3 times.

Unlock Elemental Hero Neos:
Complete 'Ancient Sacred Wyvern' 3 times.

Unlock Explosive Magician:
Complete 'Ally of Justice Decisive Armor' 3 times.

Unlock Fabled Ragin:
Complete 'Evil Hero Dark Gaia' 3 times.

Unlock Fossil Dyna Pachycephalo:
Have 666 or more Summons.

Unlock Garlandolf, King of Destruction:
Play for 50 hours.

Unlock Gigaplant:
Summon Blackwing - Silverwind the Ascendant.

Unlock Gladiator Beast Gyzarus:
Summon Gladiator Beast Heraklinos.

Unlock Gravekeeper's Visionary:
Complete 'Jurrac Meteor' 3 times.

Unlock Green Gadget:
Complete 'Power Tool Dragon' 3 times.

Unlock Harpie Queen:
Win by using the effect of Vennominaga the Deity of Poisonous Snakes.

Unlock Hundred Eyes Dragon:
Complete 'Ojama Yellow' 3 times.

Unlock Judgment Dragon:
Summon Judgment Dragon.

Unlock Locomotion R-Genex:
Summon Flying Fortress SKY FIRE.

Unlock Lonefire Blossom:
Complete 'Gungnir, Dragon of the Ice Barrier' 3 times.

Unlock Majestic Red Dragon:
Summon Majestic Red Dragon.

Unlock Naturia Beast:
Complete 'Reptilianne Vaskii' 3 times.

Unlock Raiza the Storm Monarch:
Complete 'Lava Golem' 3 times.

Unlock Stardust Dragon/Assault Mode:
Unlock 50% or more Duel Bonuses.

Unlock Supersonic Skull Flame:
Complete 'Mist Valley Apex Avian' 3 times.

Unlock Swap Frog:
Complete 'The Dark Creator' 3 times.

Unlock The Immortal Bushi:
Complete 'Naturia Landoise' 3 times.

Unlock Worm Zero:
Highest damage is 10,000 or more.

Unlock XX-Saber Hyunlei:
Win 10 duels in a row.

When you have collected 90% of ALL the cards you will be able to have one 'Forbidden' in the deck.

Unlock Yusei's Hybrid Disk:
Defeat Yusei 10 times.

Unlock Yusei Jacket:
Defeat Yusei 10 times in Turbo Duels.

Unlock Black Bird Disk:
Defeat Crow 10 times in Turbo Duels.

Developer : Konami
Publisher : Konami
Platform : Nintendo DS
Genre : Card Battle
Mode : Single-player, Multiplayer