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Bowser's Ultimate Adventure is a action-adventure game which is rated T for violence and blood.
The story starts in the year 2010 with a squad of Koopas storming a Mushroom facility in order to stop Dark Bowser from entering a time displacement machine. However, they are no match for Dark Bowser's superior capabilities and all are gruesomely killed.
Meanwhile, The Koopalings(including Bowser Jr. and excluding Wendy) ambush Dark Bowser who was responsible for the death of the real Bowser. A Koopnician revives Bowser to be sent back from 2020 to 2010(which is the current year) to protect the Koopalings. Bowser, with the assistance of his army, manages to fight his way to the main gate of the Koopa bunker and he enters the time displacement machine.
In the past, Bowser rescues the Koopalings from the dark Bowser imposter, and informs them that Koopa Day is to begin within the next few hours. He plans to steal his Koopa Clown Car from a nearby military base, and fly his children to Bowser's secret lab, a bunker that will ensure their survival during the nuclear blasts. As they arrive at the base, Dark Bowser reappears, and hits Bowser into a prototype time machine: he is sent back into the present, arriving in the current world where the Koopa Army and himself has triumphed.
Bowser once again fights his way through the Dark Koopa castle and sends himself back to 2010. He appears just in time to fight off Dark Bowser while the Koopalings escape to Bowser's lab. At the bunker, Bowser prevents Dark Bowser from reaching the Koopalings by blocking his route to them. He places a Bob-Omb in his mouth, resulting in a large explosion that seemingly kills both Bowsers.
Following Koopa Day, Bowser Jr. removes the brain from the destroyed Bowser's skull. The story then shifts further into the war, where Bowser Jr. is leading the Koopa army. He uses the brain to revive Bowser, who is revealed to have been transformed into Giga Bowser. Bowser then stomps out into battle, aiding Bowser Jr. once again. After the war, the game closes with the final caption by Bowser(now back to his normal form): The battle is finally over...