Chapter 6

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The Ancient Minister watches Galleom's Subspace Bomb from back in the desert and exhibits an increasing degree of sorrow over how R.O.B.s must be sacrificed for each bomb. He is roused by one of Pit's arrows, which he dodges as the group resumes their chase. After a short while the Ancient Minister deploys the bomb he was carrying, which the Smashers fail to stop, and so must escape as several nearby R.O.B.s are destroyed.
Diddy Kong and Fox continue to travel east through the jungle and reach a more swamp-like area. As they move on, Bowser successfully nails Diddy with a Dark Cannon shot from a distance, and sends in a troop of Shadow Bugs to clone him. Fox is about to face a two-on-one when Falco shows up, punts the Dark Cannon out of Bowser's hands, and destroys it with two Blasters. Bowser is displeased and leaves in his Clown Car, but first commands many more Shadow Bugs to merge with the existing Diddy clone, rendering it significantly larger and stronger. Fox revives the real Diddy, who is shocked by the humongous clone. Together with Falco, they defeat the imposter. Diddy then physically convinces Falco to join them in their goal of saving DK, and the trio continue through the swamp. Upon reaching a cliffside waterfall, they spot the Smash Skiff, which takes off towards the Isle of Ancients with DK's trophy on board. Diddy grunts in anger thinking the chase cannot continue, but Falco has a plan and summons the Great Fox.
Samus and Pikachu continue through the research facility. Upon reaching the room with the Power Suit, two Shadow Bug clones of it appear. The pair defeats the fakes, and Samus suits up as they continue to move through the facility. Suddenly, Ridley appears and bashes Samus against the wall. Pikachu attacks Ridley and frees Samus with Thunder. Although Samus is hurt, she and Pikachu fight and defeat Ridley. Afterwards, they find an exit to the Isle of Ancients' surface, alongside another exit with R.O.B.s carrying Subspace Bombs out of it. They decide to enter it.
Elsewhere on the Isle's surface, near a different set of ruins, Olimar is attempting to topple a giant R.O.B. with a hoard of Pikmin. The R.O.B. awakes and shakes all the Pikmin off, killing most of them. Olimar backs away in fear as a red Pikmin points to the Blue Falcon screaming in from the distance. Captain Falcon erupts from it as he delivers a Falcon Punch to the robot's head, easily knocking it over - and killing all but one of the remaining Pikmin. Despite this, the two captains team up and make their way towards the edge of the island, where they see the Smash Skiff with DK on it coming in. An Arwing flies overhead and drops Diddy onto the transport, who knocks off all the Army members currently onboard, as Falco signals success and flies elsewhere. Falcon picks up a terrified Olimar and leaps off the island, landing on the Skiff as Diddy revives DK - who easily breaks free of his chains and is ready to fight alongside the other three as troops try to protect the transport. After the enemies are defeated, the Skiff continues its programmed course into a hangar of some sort into the isle.

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