The Crystal Tower is the first Alliance Raid of the game. It was released during the A Realm Reborn patches, and its story has an impact on future happenings in the game. The Crystal Tower sequence was heavily inspired by the story of Final Fantasy III, but the story has been adjusted to fit in with FFXIV's lore.
Final Fantasy XIV is VERY story oriented, not only in its Main Scenario Quests (abbreviated as MSQ) but it has tons of side quests and other content that helps flesh out the world you're playing in. Capturing EVERYTHING is beyond the scope of this project, but I hope to at least conceptualize the MSQ, so that both non-players and players looking to refresh their memories can understand the story. Because of the important of The Crystal Tower to future MSQ, I have chosen to write a summary for it as well.
Eras before A Realm Reborn takes place, there lived the Allagans, who had wondrous technology. That technology was largely lost to time due to the various Calamities that have occurred over the years. However, during the latest Calamity, a relic of the Allagan empire unearthed itself: The Crystal Tower.
The investigation into the tower is led by the Sons of Saint Coinach, aided by Cid Garlond. Before they can enter the tower, however, its strong elemental defenses need to be breached. To do so, you need to find flawless elemental crystals, one of each of the four elements. They are to be found in the beast tribes' strongholds, so the Warrior of Light (that's you) is tested with retrieving them.
You do so. Upon returning, you find the Sons' leader (Rammbroes) is worried as he had sent an acquaintance to gather aethersand -- also needed to break the Tower's defenses -- and that acquaintaince is yet to return. So you're sent out to find aethersand yourself.
Your chase leads you to Urth's Gift in the South Shroud. While there, an unseen observer tells you he has alreayd collect4ed the water aethersand, and challenges you to a race to collect the wind-aspected aethersand held by the Ixal.
You succeed in securing the wind aethersand, but your challenger speaks up again from the shadows, and says he has a prize for you in Proud Creek.
Once at Proud Creed, you find the water-aspected aethersand the challenger had claimed before you, and he speaks now, saying the two of you will meet again at Saint Coinach's Find.
You return to the Find, where Cid uses the aethersand and crystals to make a set of "fangs" that can penetrate the Tower's defenses. It's then that your challenger reveals himself: a Mi'Qote named G'raha Tia, whose right eye is red in hue.
It turns out G'raha is a scholar of the ancient Allags, and declared himself to be expedition leader. It's now time to see if the fangs work.
So the party approaches the Eight Sentinels standing guard in front of the tower, and one by one, carry the fangs to the barrier. Upon interacting with the barrier, the fang causes the two sentinels connected to it to crumble, letting the party proceed further in. Once all four fangs have done their part, you now stand at the base of the tower. But there is still an obstacle to surpass before you enter the tower itself: the Labyrinth of the Ancients. The Warrior of Light is tasked with ridding the maze of anything which might pose a threat for the survey team.
Having done so, the expedition team comes up behind you at the end of the Labyrinth. Cid remarks that the tower is impressively huge, and G'raha says it was made to store the energies of the sun. He then turns to you to say the defenses in the Labyrinth must have been tough.
Upon your description of a "giant of a man holding a shimmering scimitar", he says this must have been Phlegethon, a hero of the Allagan revolution. Cid is skeptical of G'raha's knowledge, but G'raha says he has studied the scrolls, and the ancient texts claim that the Crystal Tower is defended by the champions of eld, resurrected and augmented through the Allagan's technology.
G'raha then suggests returning to camp to discuss the team's next move before breaching the tower itself.
Back at camp, it is determined that the Tower was not simply thrust above ground by the Calamity but has been re-awoken, based on your experiences in the Labyrinth. If the Tower poses a danger to the world (which seems likely) then it must be returned to a dormant state. To understand how the mechanisms work, the team will need to enter the tower itself. Cid is tasked with studying the Tower before everyone steps inside, and G'raha warns you to keep your fighting skills sharp as they'll probably be needed.
Upon returning to Saint Coinach's Find at a later date, you're told that the Tower possesses a gate that refuses to open. While the t4eam tries to find a solution, two strange people arrive. They introduce themselves as Doga and Unei, scholars of the ancient Allag sent to the camp by the Students of Baldesion. Rammbroes is suspicious of them, but relents to let the join the team at G'raha's behest.
The party makes it way to the gated door, where Cid stands pondering it. Cid has tried every method he could think of to open the door, to no avail. The only clue we have, he says, is the elaborate device carved upon it: a man and a woman, respectent. Allagan royalty, by Cid's judgement.
At this, Unei and Doga turn to each other and nod. They approach the door. They hold out their hands, and a light runs up the door. The device on the door glows, and the door opens.
The party reacts in shock, and Cid asks them, "What... what are you?"
Before they can answer, an unseen speaker recites a poem which predicts what just occurred, and says he is delighted to see things happened exactly as passed down through the legend. This is Nero tol Scaeva, formerly of the Garlean empire, who survived at the Praetorium. He assures the party he's no longer a threat, and has been wandering Eorzea ever since.
Cid is very suspicious of Nero's intent, but Nero offers information as a gesture of goodwill: that Unei and Doga are living keys born of Allagan ingenuity -- in other words, clones.
At this, the two clones apologize, saying it was not their intent to deceive but to prevent alarm at what is a rather outlandish tale. They suggest retreating to the Eight Sentinels to speak further.
At the Sentinels, the two clones say they are copies of two individuals who claim direct descent from Emperor Xande, the founding father of the Allagan Empire. Xande desired to bring the world under his rule, and would use any means possible to do so. Fearful of this, the original Unei and Doga made their clones to prevent Xande's plans from happening. The two clones intend to stop Emperor Xande, who still resides in the tower, but will need your help to do so.
Xande had played with forbidden powers, and had made a dark covenant with the void. Although you are successful in defeating Xande in the tower, the clones' attempt to undo the dark covenant fails, and they are pulled into a rift opened by the Cloud of Darkness. Nero, who had his own unknown plans for the clones, tries to save them but is sucked into the rift as wel.
Since Xande's dark covenant is still in effect, it poses a threat to the world: all shall be lost if the Cloud of Darkness is unleashed on Eorzea. The t4eam furiously works to find a way to save Unei and Doga, who have the power to break the covenant. Cid and his engineers succeed in opening a gate that allows you and G'raha, along with a party of adventurers, to enter the World of Darkness and save your lost friends.
After defeating the Cloud of Darkness, G'raha cries out for Unei and Doga who can't be found. Nero walks up behind you and G'raha, tsking at G'raha for the noise he is making. Nero is carrying a passed-out Unei, and he's glowing purple, as if encrusted with crystals.
When G'raha asks Nero what happened to him, it's Doga who answers: Nero's wounds were too deep and alllowed the darkness to enter his body. It appears Nero was wounded as he fought to protect Unei and Doga from other voidsent.
Unei awakes, but the Cloud of Darkness does, too. Unei and Doga tell you to flee while they stay behind in an attempt to break Xande's covenant. G'raha tells them this is madness, that they must flee too because only they can protect the world from the darkness.
Just then, the Cloud of Darkness unleashes a bolt of energy at G'raha. G'raha puts up his arms to shield himself, the the energy bolt diverts around him. Everyone is amazed. It turns out that G'raha's red right eye is proof that he, too, is possessed of royal Allagan blood. Unei tells him that he has been granted authority over the Crystal Tower. Unei and Doga share their blood with G'raha, and his left eye now turns red as well.
The two clones then urge Nero to flee as well, though Unei gives him his communicator, which he dropped while protecting them.
The three of you run to the portal. G'raha and you make it, but the portal starts to close before Nero can leave the World of Darkness. Suddenly, the crystal encrusted on Nero's body falls away -- proof that Unei and Doga were successful in breaking the covenant. With renewed strength, Nero runs to the portal, and just before it closes completely, Cid reaches through it and grasps Nero's arm to pull him through.
The team reunites with Rammbroes who declares that the tower should now be sealed, but G'raha asks for a moment to rest first. G'raha urges you on back to the Find while he stays behind to do one small thing before joining the others.
You return to the Find, but soon a researcher dashes up who says G'raha has been ordering everyone out of the Tower. Racing back to the Tower, you discover that G'raha intends to use his blood to seal the gates with himself inside. He will put the tower back in slumber. For he remembered his ancestor's wish: that the tower would become a beacon of hope in the future. Someday, when the world has caught up to the ancient Allagans in technology, the tower will be awoken again. Biggs and Wedge tell G'raha that day will only be a few years away. The doors of the tower then close, showing G'raha walking deeper into the tower.
There is one last scene with Nero that I forgot to re-watch, so I don't remember it all but I know he throws his communicator into the sea of clouds in front of the Tower, and says something like he still has plans for the future.