There’s some overlap with this and a Trivial Mystery. Head to the third beacon as if you were going to use the teleporter. Instead of using it, go behind it, and leap down. Keep making your way down until you reach a Barrier Breach. Activate it, and work your way up the steps to a True Sight totem.
Activate that, hop across the platforms, and you’ll enter an area with a permanent slow debuff (for now. Next week’s reset should change that). Re-activate True Sight if it expired, and jump up the platforms to the chest containing the first Enigmatic Mystery.
Destiny 2 Enigmatic Mysteries | Shipyard Secrets
Head back to the first beacon for this one. Leave the building, and go straight ahead until you see the True Sight totem. Continue following the platforms, reactivating True Sight as necessary, until you reach the chest with the Enigmatic Mystery.
There is a third mystery YouTuber December discovered how to reach. There’s a third chest to your left that you can spot while reaching the Shipyard Secrets chest, but you’re technically supposed to wait until next week to get it.
If you’re a Warlock with Dawnbreaker and a sword, though, December found you can jump your way over to it now. Whether it’s worth the trouble is up to you.
If you’re still working your way through this week’s Destiny 2 updates, check out our overview of the new Atlas Skews locations and how to find the Debris of Dreams beacons.