When it is in the sand, it will periodically raise its mouth and tongue out of the sand. This thing is just begging for it! You can target the tongue and Hookshot it to bring it to you, then slice it.
At this point, the monster will let loose some larvae. These will repeatedly dive in and out of the sand and may hurt you. However, their main purpose is to mess up your aiming at the tongue. Lock-on to them and Hookshot and hit them twice to kill them. They may drop refills.
Molgera has two main attacks. Whenever it is in the sand, you’ll notice that it has the sand moving towards a hole or something its burrowed. Well, if you get too close, it will swallow you and do TWO hearts of damage (not 2/4, just TWO). The other attack occurs whenever it flies around the room.
It will try to burrow onto you. I’ve never had it happen to me, but I’d avoid it anyways, seeing as a simple swallow takes two hearts. To avoid it while in the sand, simply stay away, and, while it’s moving, watch out for when the sand begins to darken and lower: Molgera is about to rise there! It will take about four sword combos or so to defeat the boss.
After exterminating this worm, Molgera will rise out of the sand, sending green blood everywhere. In the middle of the air, Molgera will turn to sand and explode from back to front, dropping a complete Heart Container . The sand recedes and the Triforce platform appears. Grab the Heart Container then step into the blue light.