Bowser, sometimes known as King Koopa, is the main antagonist of both the Mario series as a whole as well as all of the 3D Mario titles. He repeatedly kidnaps Princess Peach in many of Mario's adventures and he's also attempted to conquer the Mushroom Kingdom and even the entire universe! His main abilities are fire breathing and being able to survive perilous drops in lava, causing him to turn into Dry Bowser.
In Super Mario 64 and Super Mario 64 DS Edit
While Mario is en route to Peach's Castle, Bowser invades it, steals all the Power Stars, and kidnaps Peach. Mario is required to find a certain amount of Power Stars in order to reach Bowser in three different locations: the Dark World, the Fire Sea, and the Sky.
The only way to defeat Bowser in all three of these battles is to grab his tail and throw him into a spiked bomb. In the Fire Sea, he has the ability to tilt the platform both him and Mario re standing on and in the Sky, he can use a shockwave attack. His Dark World battle is relatively simple compared to the two others. He can warp from one section to another in the second duel and cause the platform to break in the final one.
In the remake of the game, even though Luigi, Wario, and Yoshi are playable, Bowser still only accepts Mario as his true opponent. At the end of the final battle, Bowser disappears into thin air and allows Mario to collect a Grand Star, despite only giving him a key in the previous two battles.
In Super Mario Sunshine Edit
Though it could be argued that Bowser's son, Bowser Jr. is the main antagonist of the game, Bowser is essentially the one pulling the strings. He convinces Jr. that Peach is his mother, causing the rambunctious tyke to continually kidnap Peach as well as frame Mario for all the graffiti on Isle Delfino.
Mario doesn't encounter Bowser until the very end of the game when both him and his son are relaxing in a large hot tub with Princess Peach. When Bowser spots Mario, he accuses him of ruining their family vacation and the fight begins. The Koopa King stays in the hot tub the entire battle, attacking Mario with gusts of flame and throwing some of the slime from the tub at him! The battle is quickly finished and Bowser and Bowser Jr. fall from Corona Mountain.
Bowser reveals to Jr. that Peach actually isn't his mother and he was just telling him that to get him to carry out his plan. Bowser Jr. then remarks that he already knew this but he is quite eager to fight Mario again.