Scroll #1
Fairy Upgrade
You’ll need the Cyclone Boots or the Seraph Shoulders to jump to the high ledge across the gap and reach this Brotherhood Ark.
Scroll #2
Shadow Magic Gem #1
Just ahead of you once you enter through the temple doors.
Light Magic Gem
From the corpse where you just picked up the Shadow Magic Gem, look to the left. There is a portion of the wall you can bring down using your chain. After doing so, climb the wall, and leap over the gap to find a corpse holding this Light Magic Gem.
Shadow Magic Gem #2
When you use your Warg steed to climb up the vines, you'll end up in a room with three exits. The one to the right leads to a balcony with a corpse holding a shadow gem. You can kill your Warg and pick it up now, then choose to restart from the last checkpoint. You'll be back on the Warg, and the Gem will still be in your inventory.
Hint Scroll
You can find this scroll where you find one of the fairies (probably the one you find first), at the top of a tower. The corpse is right next to a Neutral Element Fountain.
Life Magic Gem
Scroll #1
Life Magic Gem
Shadow Magic Gem #1
After you sprint-jump over the broken bridge, you'll see a small wall to your right. Use your Shoulder Dash to break it down.
Grab the gem from the corpse on the other side.
Light Magic Gem #1
Just over the second gap that you'll need a sprint-jump to clear, there is a chain grip point.
Climb up here, shimmy right, and continue up the rock face.
Scroll #2
Fairy Upgrade
Come back to this area after you’ve obtained the Stake upgrade. You can use it to open a gate and reach a Brotherhood Ark containing a Fairy Upgrade.
Scroll #1
Light Magic Gem
There's a corpse to be found up the stairs, just behind the giant crow's head.
Shadow Magic Gem
When you make your way outside, you can climb up the cliffs to the right, or drop down and jump to the left.
Take the latter path, and eventually you'll be in a cave full of small trolls, coffins, and of course, a knight's corpse.
Holy Water Upgrade
After you defeat the second trio of Swordsmasters, run up the winding stairs and you'll see an Ark across the gap. You’ll need to come back with the Cyclone Boots and the Seraph Shoulders, and execute a sprinting double jump.
Life Magic Gem
Scroll #2
