When you find the grave of William and Katherine, you can put the orchid on it and Katherine will appear before you. She will activate the red gem on Brandon's amulet which allows him to turn invisible. At the gate to the castle, use the invisibility spell when unlocking the gate with the Iron Key or the gargoyles will spit acid all over Brandon.
Castle Kyrandia is a big place so stay on the main floor for now. At the great hall, you will find locked double doors. Two keys will be needed in order to unlock them. In the kitchen, you can find the Royal Scepter hanging over the table. In the library, investigate the fireplace to discover a secret passage leading to the dungeon and the crown stuck on the other side. If you go back into the library and pull out the books in order by the first letter of their title to spell the word 'open', the fireplace will spin around without Brandon having to go along with it. Back in the dungeon, you can get past the forcefield that blocks your way by using the blue gem on Brandon's amulet. One of the rooms behind the forcefield has a loose floor tile that can be moved to discover a gold key.
On the second floor, you can look through the royal mystic's bedrooms but Herman will show up to stop you. If you get near him, he will cut Brandon right in half with the saw so use the yellow gem on Brandon's amulet to put him to sleep. Inside a bedroom on the west side is a bell stand that can be played. If you strike the bells in the correct order, the last gold key will be revealed behind the painting. The correct order is Do, Fa, Mi, Re, or green, white, gold then blue. Now that you have both gold keys, you can unlock the door in the great hall and enter the foyer.
You will see 3 pillows where you can place the royal artifacts. The correct order is scepter, crown then chalice. With the doors to the Kyragem opened, Malcolm will show up to confront you. When he follows you into the chamber, he will prepare a magic spell. Immediately go in front of the mirror on the right side of the room and use the red gem on the amulet to turn invisible. Malcolm will shoot his spell at you but it will bounce off the mirror and hit him instead, turning him to stone.
With Malcolm defeated, Kyrandia is safe once again!
Summary
Place the orchid on the grave to get the red gem on Brandon's amulet
Use the invisibility to sneak past the gargoyles and unlock the gate
Get the royal scepter from the kitchen
Get the royal crown from the library fireplace by pulling out books in order of first letter of their titles to spell 'open'
Use the blue gem from Brandon's amulet on the forcefield in the dungeon to get past it
Find the gold key under a loose floor tile past the forcefield
Go up to the second floor and use the healing spell on Herman when he shows up
Play the bells in one of the bedrooms in the correct order of Do, Fa, Mi then Re then get the gold key behind the painting
Unlock the double doors in the great hall with both gold keys
Place the scepter, crown and chalice on the pillows in that order
Use the invisibility spell in front of the mirror on the right side of the Kyragem chamber to reflect Malcolm's spell back at him