Like all the dungeons in new exotic catalyst.

Sundered Doctrine has two secret chests, and like all dungeon/raid secret chests, they can only drop loot from the dungeon/raid that the player has already collected. This means if you've only done one encounter and you get gloves when you head to a secret chest, you'll get gloves no matter what, like I did. Repeated drops are annoying when you're looking for god rolls of the new dungeon weapons, but like all dungeons, you have to have some patience to get the reward you're looking for.

Secret Chest 1: After First Encounter In The Maze

Find This Chest After Destroying Darkness Shards

After the first encounter, you'll head further into the Pyramid by following the steps downward and dropping down off either side of the stairs. Follow the path until you drop down into a no-light zone; this is the maze.

Now that you're in the maze, you're looking for three Darkness shards, which you'll need to break in order to spawn the secret chest. The shards are in the following locations, starting from where you drop into the maze:

1. Head all the way forward, then take a left. Drop down into the little pathway, then look immediately to your left to find the first shard. The shards are the same ones that appear in the Rhulk encounter of Vow of the Disciple, so those familiar with the Pyramid will know what to look for.
2. Looking at the spot where shard one was, turn to your right and crouch underneath the ageway. Turn left here, sliding under another little ageway like the one you just went through, then follow the path until you reach a larger hallway. Instead of heading down this hall, take your first right into the partially filled hall with dirt and stone. Crouch under a few more small ageways until you can't walk further, then look to your right to find shard number two.
3. From shard two's location, return to the big hallway you were just in. Use the yellow square on the wall to your right to get your bearings, then head directly away from the square and take the hallway filled with rocks to your left. Crouch through one small ageway, then turn 180 degrees around and look up. The shard should be a bit above and behind you.

Once you've found and broken all three Darkness shards, the secret chest should appear back in that main hall opposite the yellow square. It can be found by returning to said hall from shard three and looking left. Now that you've picked up the first secret chest, head forward to the second encounter by going back towards the yellow square, taking the rock-filled hallway where shard two was. Instead of going through all the crouching ageways, jump up onto the first one and follow this path.

You'll know you're on the right path here if you see stacks of barnacle-like bones/Hive residue in the corners.

Follow this path without deviating until you reach a dropdown, then continue following until the second encounter. This one's a doozy, but with the right fireteam, you should be fine. The second secret chest is after the second encounter, so watch out once you complete this tricky puzzle.

Second Secret Chest: Another Lens Puzzle After The Zoetic Lockset

Use Your Lens-Focusing Skills To Open Worm

A while after the second encounter, you'll head through a room with a bunch of hive Worm carcasses, specifically through a ribcage that leads to a larger room inhabited by some Grim. In this room, you'll notice a bunch of lenses like the ones used in the first encounter and two wheels, one with the symbol for Worm and one with the symbol for Enter. Like the first encounter, you'll need to find the Resonance source that reads Worm and use the lenses to connect it to Worm and Enter to Enter for each of the tasks in this room to be complete.

The lenses in Sundered Doctrine have small markings around the base that indicate the direction in which they can point, just like the psion puzzle in The Final Shape's "Temptation" quest.

Enter allows you to progress forward through the dungeon, while Worm causes the second secret chest to spawn. To find the chest, look around the room for a large worm carcass whose mouth is open upwards. Using the room's geometry, jump upwards and into the worm's mouth, where the secret chest has appeared. This is the second and final secret chest of Destiny 2's newest dungeon, Sundered Doctrine.