There are currently 4 missions in Destiny, including The Dark Below, that are not replayable; you finish these missions, and they disappear from the Director.
These missions include:
[b]A Guardian Rises[/b]
-The very first mission of the game after the opening cutscene, where you fight through the wall to try and find the old jumpship that takes you to this city. This mission should be made replayable, not just at the default Level 1 difficulty, on but on Level 20, Level 26, and Level 30 with the Heroic modifier active. The beginning and ending cutscenes (including the one where your Guardian arrives at the Tower) should play as well.
[b]Eyes of the Forsaken[/b]
-This is a quest mission given to you as the last part of the "Urn of Sacrifice" quest given to you by Eris. It takes place on the Moon, and has you going back to The World's Grave to stop a Hive ritual, and also includes another opportunity for your whole Fireteam to play with the Sword of Crota at the very end.
[b]Awoken Cutscenes[/b]
-These aren't missions, obviously; but these were my favorite moments in the game story-wise, and it's a shame you can't watch them again with your own Guardian. I forget the names of the cutscenes, but there's one you get after completing "the Stranger's Call" and another after "Eye of a Gate Lord". Make them replayable.
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Agree with the first two. For the third one are you talking about when you return to the Queen and her brother after defeating the gatelord on Venus?