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After Mario and Olivia obtain the key to Bowser's throne room from Luigi, as Mario is grabbing the key from his pocket, Handaconda snatches Olivia away. When Mario walks through the hall leading to the throne room, Handaconda ambushes him and engages in a battle.
In the first phase, Mario is without Olivia, making landing on the Magic Circles pointless. Mario must use hammer attacks from the second closest ring until Handaconda loosens its grip on Olivia. Attempting to attack it by jumping will make it grab Mario and throw him, and attacking from the closest ring will make Handaconda push the attack panel away.
Once Olivia is freed, the second phase of the battle begins, and all panels except for the Magic Circles disappear, which turn into a rock, paper, and scissors icon. When Mario lands on one of these spaces, he will use the 1,000-Fold Arms to challenge Handaconda to a game of Rock Paper Scissors, using the panel he landed on. Handaconda predicts its attack by having its hand out for paper, closer for rock, or two fingers out for scissors. However, it may trick Mario into playing the wrong hand when half of its health is depleted, indicated by switching its hand movements during Mario's turn. If Mario wins, he will rush attack Handaconda. If Handaconda wins, it will attack Mario. If it is a tie, Handaconda's hand will get bigger for the next turn, making it deal extra damage. The closer Mario is to Handaconda during the game will make him deal more damage during his rush attack, but leaves him with less reaction time if he loses.
Once Handaconda is defeated, Mario is able to enter the throne room and fight Scissors, who sends out Paper Mistake Buzzy Beetle.
- Handaconda is a play on "hand" and "anaconda".