This is story related and cannot be missed.
*** Spoiler - click to reveal ***Towards the last few hours of the game, you will have to gain access into Castle Lupia to progress the story. The draw bridge is UP so you can't use main door.
The secret entrance is below the altar in the sanctuary which you can open by tackling it as the lion.
In here you must bring all 3 ancient relic which are:
- Rock Axe: left of you brother's magic shop Westernmost skullrock beach. Go underwater and break the blocks with your newly acquired mace to gain access to puzzle area.
- Salamander cross: left of the old owl's observatory. You will solve the puzzle using the observatory's telescope and imitate the constellation you see there on the puzzle
- Ocarina:Deepest point of Misty Woods, right of were you fought the boss there's a block you can destroy with your mace to access puzzle area.