The Citadel – Catalyst – 2187
Shepard's eyes slowly opened, as blood slowly leaked out of her mouth, her entire body aching as if it was set alight. She slowly looked down to herself; wearing the shattered, scarred remnants of her armour, turned black with soot and ash from the war below. Her skin was likewise coated, as blood dripped out of wounds both fresh and reopened. She then looked away, to the titanic chamber. It was unfamiliar, and judging by the massive arms reaching into the distance, it was seemingly in the very centre of the Citadel. Many thousands of Reapers clouded around the Citadel, around the Crucible, as many others flew down to the Earth. Shepard looked away, closing her eyes, trying to drown out the pain.
"Why have you come?" Her eyes shot open, as a light, strangely ethereal voice pierced into her mind. She groaned, as she slowly rose to her feet, her left hand clutching around her abdomen, as she stood up. She gave a heavy cough, as she spoke, not expecting a reply.
"Wha-… Where… Where am I?" The voice, contrary to her expectations, replied.
"The Citadel. My home. Why have you come?" She turned her head, trying to find the source of the voice, only to see nothing. She gave a huff as she silently thought to herself.
'Must be out of my god-damned mind now… Delirious hallucinations from blood-loss… Alright, I'll play along.' Shepard spoke, her voice distant.
"I'm here to destroy the Reapers. Can you, whatever you are, help me?" The voice gave a reply, genuinely confused.
"I have no reason to aid you. The Reapers are a solution." Were Shepard not suffering blood-loss at the time, rage might have set in. Now, she only felt weary resignation.
"A solution to what?" The Voice replied again, as if she should already know.
"To Chaos. To ruination. To the death of all Organic Life." Shepard fought off the urge to black out, to let the darkness take her, as she spoke again.
"The Reapers kill off trillions of organics every cycle. How in the fuck is that a solution to extinction?" The voice gave a retort.
"The Reapers guard against the rise of Synthetics. Had the Reapers not acted previously, Synthetic Life would have purged everything; not just those civilizations of sufficient power." Shepard shook her head, hardly believing the entity's explanation.
"You're…" She gave a cough, blood spurting out of her mouth. "You're crazy. Must be stopped. I'll… I'll find a way." The voice spoke up, as calm as before.
"No, you will not, Shepard." Her eyes widened as the entity spoke her name; it knew her name. What else did it know? She shook her head, replying with all the confidence she could muster.
"And you're going to stop me?" Shepard half expected the voice to summon something: a Reaper, a Kinetic Barrier, Brutes, hell, even just a Marauder would do. Nothing appeared. The voice spoke, however.
"You will not be harmed, Shepard. You had charisma and wisdom far outstripping any of this cycle. You destroyed Nazara. You united the species of this cycle against us. This was not overlooked." Shepard gave a quiet growl, replying.
"So, I'll just sit here until I starve then, right?" The voice spoke, its tone remaining neutral.
"No. You will take Nazara's place." Shepard's eyes widened in terror, as she looked around the chamber for a weapon; her Carnifex, a Lancer, even a broken pipe. She gave a retort.
"No, you… you can't be! I won't let you!" The voice spoke, as Shepard began to lose strength, the blood loss becoming too hard to fight against anymore.
"You cannot fight your ascension, Shepard. Embrace it." She collapsed to her knees, as her eyes began to slowly close. She struggled, trying to keep them open, as she saw the Earth ahead; the burning Earth. She heard metallic thumps as she finally embraced unconsciousness.
"The Cycle continues."
Many Years Later
Deep Space – San'Shyuum Dreadnought 'Righteous Odyssey' – 1st Age of Discovery
"What have we discovered, Noble Prophet?" The Prelate looked to the frail San'Shyuum priest, his eyes widened with elation, as he looked out the window.
"The deliverance of the Forerunners. The truth of their power. Even the finds on our worlds pale in comparison to this." The Prelate gave a scoff. The priests of the San'Shyuum were often prone to melodrama when it came to relics of the Gods. He moved to the viewscreen to see. It would likely be a surviving Dreadnought, or another Relay, or-
The Prelate's jaw dropped as his eyes widened in awe. Quickly renouncing his doubts, he looked to the Priest, dropping to his knee, as he spoke.
"Noble Prophet, please accept my forgiveness. I have doubted the majesty of the Gods, and their wills." The priest looked down, speaking softly.
"Do not fret, my friend. The Gods will accept your forgiveness. You have always been pious in your actions. One moment of doubt will not damn you in the Great Journey." The Prelate stood back up, turning to the viewscreen as he looked at the Gods' holy relic. It was a titan in Space. Hiding within the middle of a large Nebula, the relic remained, its five arms open, as if inviting them aboard. This was truly a sign that the Gods had favoured the San'Shyuum. The Priest activated his communications device, speaking to the Bridge.
"Shipmaster, we must approach the relic." He spoke passionately, putting emphasis onto his words as he would a sermon. "This is of great importance to the San'Shyuum people, to the Great Journey itself. We must walk upon its surface."
The Shipmaster gave a response, his tone reverent and respectful. "Of course, Noble Prophet. We will approach the relic immediately. For the Great Journey." The Dreadnought lurched forward, as it began to slowly approach the titanic station, the crew becoming ecstatic. The Great Journey was ahead, and this remnant of the gods was proof of it. The Prelate looked ahead, his faith now unshakable, as the station approached.
Codex – Discovery of High Charity
In all the ages of the Covenant, none are as important as the First Age of Discovery. Beginning with the discovery of a Forerunner Dreadnought landed on our homeworld, this Age propelled San'Shyuum technology and culture ahead by centuries, as well as sweeping aside the false beliefs of lesser deities, in favour of the Forerunners. Propelling our kind into Space to uncover the secrets of the Forerunners, the Dreadnought's many technologies are seen even today; from the Plasma Rifles used by the Sangheili, to the Element Zero Cores of our own holy ships, to the usage of the Mass Relay System. However, each one of these discoveries paled in comparison to that of High Charity; our most Holy City. Found near the end of the First Age of Discovery, High Charity was a repository of ancient wisdom and technology, one which propelled San'Shyuum Technology far further than before, and laid the groundwork for the formation of our Covenant.
Arriving on High Charity, the San'Shyuum explorers found remnants of ancient Forerunner society; cities, gardens and lakes, protected and maintained by creatures now a staple in Covenant society; the Huragok. Though many traits about the Huragok remains a complete unknown, the Huragok use biotic and technological skills to build and maintain advanced technology; from new Wards on High Charity, to new weapons and vehicles. Truly, the Huragok are an example of the Gods' own gifts to us, another step on the path to the Great Journey.
AN: Well, here is an idea I genuinely haven't seen before. There are a lot of 'UNSC replace Systems Alliance' fics, a few of 'Covenant go to war with Citadel Species' fics, but not this idea.
The idea itself, I had while rewatching the Refusal ending for Mass Effect 3, and replaying Halo 2A like crazy, so I wanted to see this. The Covenant are just the next set of species in the Reapers' cycles. Because, hey, 'Civilization that goes around, picking up bits of technology from an ancient species that came before them' pretty much describes both the Citadel and Covenant pretty well. Just add a healthy dose of religious fanaticism with the Covenant, and you've got a new cycle that could fit well into Mass Effect.
A few things bear explanation, however, to explain the discrepancies between this AU and the canon Covenant.
First off, the Covenant do have ready access to their Plasma Weapons (Since they're recognizable), as well as on their ships. However, this is easily explained, and a part of the AU. Instead of a genuine Forerunner Dreadnought on the San'Shyuum Homeworld, it's a crashed Geth Dreadnought where they get their Eezo Tech and Plasma Guns from. (Though, they innovate a little bit, introducing weapons like the Energy Sword, which the Geth don't really have an analogue for).
Secondly, the Covenant history in this is no less bloody than before, though some races will be more prevalent than in canon, such as the San'Shyuum and the Yan'me. This is meant to be a way of exploring cultures that usually don't get explored too often, and how Mass Effect technology would change the way their culture works (For example, San'Shyuum revere the Biotics of their kind, seeing their abilities as gifts from the Gods.), while a few Mass Effect canon races will get a mention, such as the Rachni (Assume Shepard rescued the Breeder, rather than the Queen, and the Breeder survived the war), and the Yahg.
Thirdly, there will be a few parallels to Shepard's own journey through the story, but there will be many differences as well. Expect the more blatant parallels to end the moment Thel leaves the Citadel.