Having just played through Chamber of Night, something occurred to me.
What if, like in the Halo: CE missions, we had to leave our Ghost behind to do one task while we went and stopped a crucial Hive Seeder with a hive captain on it or destroy a major enemy on Mars?
Obviously our ghost gets captured and now, we have to go get him back with an ambush full of Majors and Ultras?
If that one doesn't go, let's at least have some fun with this thread:
In the middle of the night, Master Rahool is kidnapped from the Tower by invisible Psions. Our job is go get him back, but we don't know where the Cabal have taken him. Queue the missions to track, hunt, and obliterate all in our path. For the sake of Lore wise, the Vanguard leaders can explain they replaced Rahool with a robot with less functions. Like they can only decrypt certain engrams, but no legendaries or exotics from Xur.
So to gain back full access to the Cryptarch, we must rescue him unless you never want to get another legendary engram or exotic for that matter, deciphered.