[b]This is a list of all the secret areas I know of so far.[/b]
1. At the end of the Story mission area, proceed onwards until you come out into the open. There will be a small area with Hive and Fallen fighting each other. Go to the rusted helicopters near an edge of the area, and jump down from the ledge. You'll see a secret room with an Ascended Ogre (Hive) that is Level 11. This a pretty hard enemy, but fun to fight as it's quite a challenge and the only known Ogre in the Alpha.
2. About halfway through the Devil's Lair Strike area (past The Divide if you don't want to do the Strike) at the place where your Ghost needs to take down a barrier, look around and you will see a large entrance glowing green. Head down the winding path and you will end up in The Grotto, where a lot of ?? Level Hive dwell. It is not a good idea to attack these enemies, as they are practically meat barriers, but they are possible to kill.
3. When on Patrol, head to the Mothyards. When there, head towards the Story mission entrance (building with the large radar) and turn right before it. You'll notice an entrance to a crevice like path. Follow this path until reach the Forgotten Shore. Once there keep going straight until you pass the big building at the far side, where you'll see another entrance. Head along that path, avoiding the two ?? Level enemies (unless you have the time and patience) and you'll reach The Hot Gates (300 reference?). There a lot of ?? Level Fallen here protecting a Hive cave entrance. [b]EDIT:[/b] (from user The Mandalore) At the Hot Gates, if you proceed into the Hive Cave you will reach the Hidden Swamp, where another Hive Ogre is!
4. When on Patrol, head right from spawn until you see a staircase along the far wall. Head up this staircase and pass through the building that follows. Soon you'll reach The Divide. Once here, go right and along the path, until you see a large glowing orange entrance to your right. Head into this area and you'll end up at The Cosmodrome. This is a special area, where the first gameplay of Destiny was released back at E3 2013. You'll find yourself at a barren wasteland, and you should see to your left a sign that's fallen over. Sit down on this sign and take a screenshot, as is the trend! The view at this area is amazing, and if you're like me and watched the first gameplay a million times, it's a very cool feeling to walk through the exact same steps as Jason Jones. You won't trigger the same mission, but there is a jumpscare where a light literally explodes off the ceiling, and ruins your moment of nostalgia and awe.
These are the only secret areas I know of so far, so comment any other areas I may have forgotten or that you've found out! Also, have fun with Destiny!
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This has been the best part of Destiny for me, by far. Four solid — solid — days of playing on the same map and even up until last night still finding new areas and corners to explore. There's just so much effort on display here I'm frankly amazed. I was three days in before stumbling onto the the Forgotten Shore and the outer wall/ Cosmosdrome areas ( I know a lot of people got there much quicker :) ) and when you talk about nostalgia and awe (nostalgia for something we've seen but not experienced firsthand) you hit the nail right on the head. Walking out to see all of those rusted, burnt-out cars, and turning around to see the wall was just amazing. I took a lot of screenshots there. And last night we found the Ogre by the helicopters. He lunged at me and fell off the cliff for the easy win I guess. :)