Mothula's boss chamber consists of a moving floor surrounded by spikes. Once the boss battle begins, the floor starts shifting, and the spikes start sliding across the floor. Because of this, Link must not only worry about Mothula, but also avoiding the deadly spikes.
Mothula shoots lasers in groups of three and attempts to ram Link. While avoiding its attacks, Link can get close to the creature and use his sword to effectively take it down; the Fire Rod, which is acquired within Skull Woods, is actually a slower route to victory, as the sword will do more damage and does not use large amounts of magic. Interestingly, Link can also use a captured bee on Mothula. This proves useful because Link is able to focus on dodging the sliding spikes while the bee attacks Mothula in his place.
In the original Link to the Past for SNES, there was a bug where Mothula would take no damage from the Level 4 (gold) sword or from spin attacks from the Level 3 (red) sword. If Link obtains the gold sword before facing Mothula, the Fire Rod and the Hammer are the only effective weapons remaining to him. This bug was fixed in later remakes.
As soon as the hookshot is obtained, the Magic Cape can be found in the Dark World equivalent of the Graveyard using a glitch that is in both SNES and GBA versions of the game. In conjunction with the Magic cost reduction from Mad Batter, the cape can be used longer, and with the Golden Bee, Mothula can easily be dispatched with taking little to no damage at all.
Palace of the Four Sword Edit
In the Palace of the Four Sword, Link must face Mothula again. This time there are no spikes and the floor does not move. Instead, Mothula replicates itself. If Link attacks the fake Mothulas, they turn into bees and cause no damage to the real one. Captured bees can still be used here, for even greater effect than in skull woods, as the bees only attack the real Mothula.
According to the manga, Mothula was once a very gorgeous woman who became very jealous of another girl's beauty. She came to the Dark World to find the golden power to become even more beautiful, but was turned into this shape because of her envy.