Tristan has a good eye for strategy in the game and was organizing the resistance by himself while he waited for Yugi.
Ryou Bakura's plan to help out is to sneak into the enemy base, wait a day, and then set the place on fire to take out the cannons. He's so eager to do this that Yami Yugi can't stop him.
Tristan is the only one of Yugi's close circle of friends to resist Scott's mind control.
Yami Bakura enacts a plan so he wins no matter what happens. He gets Yugi to chase him while his army attempts to burn the resistance's capital city from behind. If he defeats Yugi and the resistance, that's one problem solved. If Yugi defeats him, Scott's army knows exactly where Yugi is and can thus strike.
Yami Yugi dismantles Scott's bluff to brainwash everyone again and calls him out on why he wouldn't make the game more unbalanced—for some reason he needs the world to be fair, and once he's in the game he can't brainwash players or spawn in armies.
Kaiba spends 90 percent of his campaign being awesome. He trolls the game characters, defeats anyone he recruits in battle, tells off Scott Irvine, and even tells off DarkNite/Nitemare.
Nitemare: I will devour every last one of your souls! You will spend an eternity in darkness and tormented pain! Kaiba: Go back to the fairy tale you come from!
In Kaiba's campaign, Pegasus approaches him in secret and asks him to join the resistance. He only accepts when Pegasus reveals he wants Kaiba to be the leader.
In Kaiba's campaign Pegasus tells Yugi about Mokuba being kidnapped, convincing him to fake a surrender to buy Kaiba the time he needs to rescue his brother.
Joey's first fight against Odion has this conversation.
Odion: You fool. If you insist on spilling the blood of your men for nothing, then so be it. There is no escaping destiny. [Joey defeats him] Joey: Destiny's not something that happens to you! It's something you make happen! You're the fool if you think someone like you who leaves everything to fate could ever defeat me!
In Joey's campaign, Mai saves him from Marik's combined forces and immediately makes a plan to bring him down. It works perfectly.
Joey has several rematches against an NPC version of Marik, who eventually wields the Winged Dragon of Ra as Yami Marik. Joey wins, leaving Yugi and Kaiba's campaigns free of a powerful enemy duelist.
This game has the only moment in the entire franchise where Joey can fight and defeat Kaiba, and the game makes sure you know it.
Kaiba: Hmph... For a bunch of average duelists, you've done quite well for yourselves. But that's about to end. Even in this bizarro world, you are no match for me. Joey: What did you say!? You're going to eat those words! And just what the heck are you doing fighting for the Empire? You jerk! Kaiba: Ridiculous as it may be, this seems to be the role I've been assigned. So until I find a way out of this nightmare, I'm going to play along with the idiot that came up with this story. Besides, you've always wanted to face me in a duel, little Joey, haven't you? It might prove very interesting to do it here. Don't you think? So, get back in character and face me! If you've got any pride at all, that is! Joey: You know what!? I've never liked you, and I'm going to enjoy stuffing that huge ego of yours down your throat!
Scott Irvine gets villainous awesome moments by going from a random technician to a force to be reckoned with, outmaneuvering the heroes several times throughout the game and manipulating them to do his bidding.
Fighting one Egyptian God with another one. The fight suddenly becomes a freaking Kaiju battle.
Defeating an Egyptian God without one, using monsters like Mai's Harpie Ladies or Bakura's Ansatsu.
In the same vein, unleashing your very own Egyptian God on other story bosses in replays of already-done campaigns. There's nothing like seeing Kaiba pull out his Blue-Eyes Ultimate, only for you to sic Obelisk on him (replying "Mine is bigger than yours!" optional), having your titan shrug off the "Ultimate" Dragon's best attacks and swat it aside with the Bitch-Slap Of Doom.