The Legend of Zelda: A Link to the Past

You'll want to use the Firerod on Mothula.

If you only have three bottles, capture 2 Faeries and use the last bottle for either Magic Medicine (green) or Cure-All Medicine (Blue). You can get the Green Medicine for free by throwing your bottles into the Faerie pond inside the Waterfall of Wishing (same place you get the Magic Boomerang and Red Shield).

The Firerod drains magic pretty quickly, so it would be a good idea to upgrade your Magic Meter before fighting Mothula. First, get some Magic Powder. Next, go to the area outside of the Blacksmith Shop in the Light World. Use the Hammer to knock down the peg next to the building, and jump down into the hole. Walk through the cave until you find a green structure that resembles an altar. Throw Magic Powder into the red liquid.

Even without bottles and special armor and extra Heart Containers and reduced magic, you can easily beat Mothula as long as you have the firerod.

Face Mothula, charge your sword, and shoot a flame from the rod. Wait for Mothula to stop flashing and shoot it again. While you are charging your sword, you can move around to avoid the spikes while holding your aim on Mothula.

If you are out of magic and desperate, you can also try to inch close to use a spin-attack. At that point, I suggest having the Hookshot selected as your special item. While the hook is extended, you become invincible.