Molgera is the second of the two monsters guarding the power of the sages that can restore the true Master Sword. Together with Jalhalla he was created a long time ago by Ganondorf himself. Molgera lives deep down in the Wind Temple and he is the one who guards the power of Fado, the sage of wind, who he killed ages earlier at the time when Ganondorf weakened the Master Sword.
When you have entered the chamber, jump down into the sand and roll straight forward to trigger the cut scene.
It is possible to skip all phases of molgera. After the second hit of each phase, if you hookshot the tongue, then have it get hit, then hookshot it again (frame perfect) you can renew the next phase immediately.
To beat Molgera you will need the dungeon item, the Hookshot. Right when the fight starts Molgera will be under the sand. After a few seconds his head will come up, and with a good aim you can hook his tongue before it is fully arisen.
The first part of this fight, or the first phase actually, is pretty casual and all you need to do is hook his tongue and slash it with your sword. The best way to deliver damage with your sword is with the use quick spins. In each of the four cycles you need to deliver three hits before the next cycle begins. The best way to do this is by stabbing the tongue once and then performing a quickspin.
After 6 HP has been taken from Molgera, he will begin a new phase of the fight. Soon you will face this giant sand worm rush himself out if the sand and fly above you in the chamber. In this phase there are two optimizations that you can do to speed up the fight. The first is to follow Molerga around the room and be very close to him when he attempts to dive at you, this will cause him to dive into the ground much quicker than if you were far away from him and thus causes him to arise again earlier.
The second optimization is keeping the camera near the wall at all times while Molgera is flying around and diving into the sand. This prevents the game from lagging and thus wastes less time.