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Morphology: Bowser
Fire-breathing bipedal dragon. Hardy and barbed carapace is extremely durable.
Due to his massive size and weight, Bowser can tolerate a number of attacks, both direct
and indirect, long before he is sent off the stage. While his movement is slow, his attacks
are fairly quick and powerful. However, he relies mostly on close-combat. Exploit this flaw
by means of long-range combat. As long as Bowser is outside of your range, he is harmless.
Ground
It seems that Bowser does better when grounded, rather than when he is aerial. He has a lot more attacks to choose from while he is on the ground, and much of his attacks can be deadly if they make contact. Because of Bowser's large size, it is only right to believe that Bowser's offense and defense are very powerful and can deal out a lot of damage in a short amount of time. Yet, due to his large size, he's an easy target to hit. When Bowser is grounded, one of his favorite tactics to perform is his Whirling Fortress (Up+B) out of his shield. This is very useful, because it's quick, powerful, and it hits Bowser's opponent upward. It also doesn't leave Bowser open so as to be punished.
Bowser's Whirling Fortress is capable of knocking his opponent out vertically if at a good amount of damage percent. While Samus is the seventh heaviest character in the game, her vertical survivability lands thirteenth in rank. The Whirling Fortress is commonly used out of shield as well, if you get too close to Bowser. Usually when Bowser uses his Whirling Fortress out of shield, he tends to be defensive. The way you can deal with this is by firing a Homing Missile at Bowser to cause him to shield. He may keep his shield up, since he will see a Homing Missile and will not desire to get hit, and he will see you coming at him. If you tend to use your dash attack while approaching Bowser, it may throw him off if instead you use your dash grab.
Aside from this if getting close, Bowser can shield-grab Samus and inflict some damage and wait for her to be released. Upon this, Bowser may use his neutral A twice, or he might use his f-tilt or d-tilt. Flying Slam (Forward+B) is also an option. It is possible to get out of the second hit if Bowser uses his neutral, and the same with his d-tilt. It probably isn't possible to get away from his f-tilt or Flying Slam, though. Try not to use your dash attack too much, and if you do, use it late. There are two reasons for this. The first reason is that if you do hit Bowser, you'll do 10% damage on him instead of 6%. The second reason is you'll end up right behind Bowser, which gets you out of the danger of being shield-grabbed.
Air
While Bowser may not be an aerial character, that doesn't necessarily keep him from attacking in the air. Bowser can perform his Flying Slam (Forward+B) and jump infinitely in the process. Don't think for a moment that Bowser will not use this if the match doesn't look like it will be in his favor. He could be at high percent while you might not be, and all he has to do is use his Flying Slam to KO you. Keep in mind, however, that the one who is at lower damage percent gets control of the momentum and direction of the Flying Slam. If you two are on your last stock, Bowser can win if he successfully executes the "Bowsercide" on you. If Bowser tends to use his Flying Slam to jump infinitely, use Homing Missiles and z-air to shut him down. Also be sure to stay away from the edge.
Two other attacks that Bowser possess are his u-air and f-air. Both are capable of KO'ing at moderate damage. If you're above Bowser, chances are, he'll try to use his u-air, which can cause Samus to lose a stock if her damage percent is in the mid-eighties to nineties. This simply makes the u-air Bowser's best aerial attack. This might vary, depending on the stage that it selected, as well as whether or not you were about to land upon a walk-through platform that is higher than normal ground level. As for Bowser's f-air, it may usually be performed if Samus is off the stage. So, in a way, it is something Bowser might use to edge-guard.
Another attack that Bowser can perform is his Fire Breath (B). It is dubbed "Wave Fire" by Dias4Flac, and is noted for being able to be used with Bowser's infinite jump. This attack can be used to punish Bowser's opponent in the air. What is more, the Wave Fire will cause Bowser to move slightly forward. If caught in Bowser's Fire Breath, use directional influence as quickly as possible, since the attack can do a considerable amount of damage if left unchecked. This might mean that Samus will be unable to use her f-air against Bowser, unless she happens to be slightly higher than Bowser or if she uses f-air first.
To take advantage of Bowser while he is in the air, you want to use your Homing Missiles in conjunction with z-air. As long as Bowser is in the air, his options are limited, since he cannot use his Whirling Fortress out of shield, let alone, perform the Whirling Fortress in a safe and unpunishable manner. Bowser can attempt to air-dodge the Homing Missiles, but since the Homing Missiles slow down and because Bowser is such a large target, air-dodging may be rendered useless. For this reason, if Bowser does air-dodge often, use the Homing Missile along with f-air or u-air, since both aerials do consecutive hits.
Edge-Guard
It seems that Bowser has a number of options to choose from when he is edge-guarding. Some are better than others. Bowser can jump out at you from the stage and use either his f-air or u-air on you. He may also decide to Bowsercide you if the player is feeling confident. That, of course, shouldn't be your biggest worry, since it might not be a common tactic to use. Fortunately for Samus players, you can execute your Bomb Jump to stall and then move toward the stage when Bowser needs to also head back to the stage. Still, you should be cautious since Bowser could try to edge-hog or simply jump off the edge and use his second jump to attack and his Whirling Fortress to return to the edge. Upon returning to the stage, it would be wise to use Samus' Homing Missiles to hinder Bowser from even attempting to jump out at you.
When Bowser is on the stage but is still edge-guarding, he may choose either to use his Fire Breath or d-tilt. Samus will be safer if Bowser uses these as his way of edge-guarding, since Samus can use her Grappling Beam to grab onto the stage. Just be sure that Bowser doesn't decide to edge-hog at the time you are going to use your Grappling Beam or your chances of returning might be minimized. If you happen to return to the edge and Bowser is right there trying to use his Fire Breath or d-tilt, remember that you can let go of the edge and use your Screw Attack to grab onto the edge again. As long as you do this, Bowser can't do anything to you, unless he decides to do something different. This is a tactic I like to use, not just on Bowser, but on any of my opponents. As a Samus player, you know your options in order to return to the stage once you're on the edge.
Edge-Game
Bowser has a few edge-games to select from. I won't bring up Bowser returning from the edge by tapping neutral A in order to hit you if you're close. Instead, there are other attacks that Bowser has that he can perform while he is on the edge. He can let go of the edge and use his second jump to perform either his u-air or f-air. These aren't really fancy attacks, and you won't have to worry about them if you're not close to the edge. Another one of Bowser's edge-game is known as "Return Fire." What Bowser does is jumps up from the edge and onto the stage, already using his Fire Breath. Again, as long as you're not close to the edge, you don't have to worry about this.
Recovery
Bowser's recovery isn't excellent in any way, at least vertically. You might liken that to Donkey Kong's recovery. (It's slightly better than Donkey Kong's.) Still, it's amazing to see how far Bowser can go with the Whirling Fortress when he is returning to the edge horizontally. Take note of this. MrEh has noted that the initial frames from Bowser's Whirling Fortress has invincible frames, so it is best to wait it out a quick second before deciding to go out and spiking him. It might just be better to use Samus' Homing Missiles and her z-air for this one, unless you really enjoy using your d-air to spike your opponents.