The silence swept over his mind like a unimaginable nightmare. It was like losing the ability to smell, to hear, to breathe. His body staggered and his world spinned as the great disconnection from the minds of all others, the perfect harmony they had experienced was shattered. For thousands of years he had shared and experienced the memories with the rest of his people. He managed to stagger out of the living and breathing building and as his eyes scanned his surrounding he saw tantalising images that would scare him forever. Bleeding Saplings, barely 100, children laying fallen, twitching. His mind became foggy unable to comprehend what had just taken place without the unity and surreal clarity of their shared mind. 

His body slowly began to regain control from his reeling mind and instinctively began moving him towards the great beating heart of the planet, the capital city. Since as far back as he could remember unable to recall with accuracy, he had never known this to happen. All this death and pain. His mind slowly lifted its dark heavy cloud of obscurity and he regained focus. He began to remember...he was part of the Senate, a advocate for peace and prosperity with others, visiting this new colony to oversee and help along its development. He was Ardel and one of few on the senate that wanted peace.

Ardel slowly approached the capital city all concept of time lost as his body finally regained control from his broken mind, instinct was all the drived him now. All around him there was confusion as old Unfallen slowly regained their minds.  He quickened his pace as his mind became clearer and clearer until he reached the very centre, an anomaly on the planet,mone that the Unfallen had hoped to study....or so Ardel thinks, everything is fuzzy, like a blur. The structure was thought to be endless and towered not above but below ground. Ardel instinctively entered and descended the winding steps to the research laboratory at the bottom. The structure hums with power like it was constructed yesterday.  As the doors hissed open his mind snapped and he fell hitting the ground cold.

Ardel awoke to the warm, homely hum of his ship in high orbit over the Home World. He remembered... nothing. A creeping sensation and nagging fear of something that could be or never was. He caught glimpses of pain, death and the future. Where the Unfallen stretch countlessly across the stars and their Empire was strong. But that fear didn't leave him, he felt the Unity of the hive mind and filed away the memories for the rest of the Unfallen to share. The Dust he had encountered a thousand years ago had left him with foresight of things that could be, maybe or could not. As Ardel began to resume his daily routine he promised himself he would lead the Unfallen to the greatness he had witnessed.

Well constructed, I can see that there is nothing glaringly wrong with your story in terms of structure and you have used a variety of words to express your narrative. The only errors on first glance is spacing between certain punctuation and the rest of the paragraph. Like this:

He remembered...nothing.

With le Space:

He remembered... nothing.

Bleeding Saplings, barley 100, just children were laying fallen, twitching.

Barely not Barley, and minor tweak:

Bleeding Saplings, barely 100, children laying fallen, twitching.

But such a thing doesn't detract from readability and its simply a very, tiny minor errors - there are only a few.

A great story nonetheless: an Unfallen with mystical prescience gifted to them through dust, visions of the future but how accurate are they? And are they fates that can be changed?

Only really one question, is the ship this ancient Unfallen Hero on another Unfallen or of Unfallen design? Or is it of a different craft altogether? Of course, I don't have any issue with an Unfallen being old and remaining relatively mobile, I intended size to be a matter of their own choice to some degree not necessarily a forced process.

Its more fun to remain unbiased anyway and see what folk run with: influences they take from my design, my spoken words during the last phase, other peoples ideas that they have thrown around, Devildog's game-play design and other bits and pieces they feel are appropriate. 

Anyway, good luck to you and I guess we will see if the fates will it.