
After you are done with Ghirahim, go to the Sealed Grounds and be ready for yet another boss fight.
Just like with Ghirahim, the second fight against the Imprisoned will not be a cakewalk. The principle is still the same - get on its head and pound the pillar with vertical strikes. However, now you have to pay attention to the shockwaves being sent out from its feet with each step. Once it starts climbing up the wall (Or sliding on its belly like in the first fight, press up on the D-pad to switch to Groose and shoot a bomb at it. Rinse and repeat until it's defeated.
After you finish the fight, open up the gate of time, cross over and talk to Impa. Once all the cuscenes are done, head to Skyloft. In the academy, talk to Gaepora. When you're done with him, talk to Owlan in the office next door. Finish the spiral charge training and head to the Lumpy Pumpkin, an island southeast of Skyloft. Talk to the owner, then head for Thunderhead, the cloud ball where you learned all the songs. Land on the rainbow island to start another boss fight.
You will not see the boss at the start. Instead, you'll have to fly around Thunderhead, following Levias and spiral charging the tentacles, popping the eyes. Once that is done, land on Levias' and be ready for the actual boss.