Final Fantasy Patch 5.3 has streamlined the original Main Scenario questline from A Realm Reborn, but a couple new requirements have been added. One of these is the Crystal Tower storyline, and you can’t wrap up the post-A Realm Reborn story until you’ve finished the quest “The Light of Hope”. This quest is at the far end of the Crystal Tower arc, meaning you’ll need to clear all three wings of the raid to move on.
The Crystal Tower quest-chain starts in Mor Dhona.
“The Light of Hope” requirement doesn’t occur till you are deep within the post-ARR MSQ, so you’ll want to plug away at the post-ARR story until it tells you to complete that specific quest. You will need to be iLvL 55 to access the first wing of the Crystal Tower raid, The Labyrinth of the Ancients, but the updated loot tables from both quests and dungeons should get you up and over this barrier.
Once you’ve reached the quest “A Time to Every Purpose” and are sitting at or above iLvL 55 grab “Legacy of Allag” from the Outlandish Man (X: 21.8 Y: 8.1) in Mor Dhona. This will kick off the Crystal Tower arc, and all you need to do is follow it to reach “The Light of Hope”. Clearing the wings won’t be much of an issue: they’re part of the Alliance Raid roulette, meaning high-level players dominate the alliances. While you shouldn’t ignore mechanics entirely, you’re likely gonna get carried. That said, there is no limit on loot in the Crystal Tower raids, so grab any upgrades you can – they’ll make later quests easier.
The story is lengthy, but I recommend watching all the cutscenes. The Crystal Tower story was made a requirement for a reason. The events in this arc play a large role in the Shadowbringers expansion, so unless you give zero shits about the story you’ll want to pay attention. Once you clear the third wing, The World of Darkness, you’ll move on to “The Light of Hope”, and once that’s cleared you’ll be able to resume your progress in the post-ARR MSQ. There are two quests that follow “The Light of Hope”, but they are not needed to move on with ARR. I recommend them for the extra story, but you can ignore them if you so choose.