Chapter 1: The Deep Breath

Mars, 2030

"Well… This is obviously an artificial structure. It's not ours." Carlos Morales stated, while closely staring at the entrance. He was a tall man, with a pale white skin and light brown eyes. His family had mostly descended from Spaniard colonizers, hence his name.

The entrance looked like an airlock, it was previously buried by sand but in the past few weeks Carlos and other astronauts were quick to remove any sand blocking the entrance. Now, it was time to investigate.

"Is this a work of the Chinese? Maybe the Indians?" Muhammad Salib suggested, he got closer to the door to examine it. Muhammad was a short person, with an olive-coloured skin and dark hair. His eyes were of a deep brown colour, and he had an oriental nose.

Muhammad touched the entrance and it subsequently opened, this caused sand to slide and both men to fall down into the structure. "Crap!" he yelled in surprise, as this happened.

After falling, both astronauts started checking their suits looking for a puncture or any damage. None found.

"What the hell is this?" Carlos raised his voice in question, as he came into the room with many monitors. In the centre, there was a metal box with a crystal orb in the middle.

"By Allah…" Muhammad mumbled to himself while looking at the orb, while he himself was not a man of faith (Actually an atheist by definition) he had been raised on a conservative Muslim household and such expression had stuck with him.

"Don't touch that, Muhammad! You will trigger something el-" Carlos was interrupted as a green fog started to form over the Crystal Orb. Muhammad had kept his hands for himself, without triggering anything. This was something which had activated without the interference of either man in the room.

The fog dissipated and a vaguely humanoid figure appeared. It had a triangular head with a large crest and four eyes, it was a hologram rather than a true xeno. Its features were somewhat insectoid and reptilian. Some sort of green light scanned the two men very quickly, and this figure spoke in an unbroken English.

"Pressurizing of the room, initiated." The alien figure said as the airlock closed. Carlos turned his head and was near-panicking as his only way out was closed. "You may take off your helmets." Both men didn't dare to expose themselves to the room's air, though.

Muhammad, meanwhile, was closely analysing the figure whose image was reflecting on his brown eyes. "Who are you?" He asked, and turned on his recording device.

"There's no need to record this conversation, your people will be free to access any and all files from this terminal." The Prothean hologram spoke. "Addressing your question, I am a Prothean Virtual Intelligence. My name is Decadence. I was designed to make interaction with this platform and this information easier."

"Can we get out?" Carlos almost pleaded, while still sitting down as he was too weak to stand up.

"Of course, the controls for the airlock are still fully functional. I will teach you how to use them shortly." Decadence stated.

"An Artificial Intelligence? This means that you are a fully self-aware machine?" Muhammad inquired, still keeping a calm stance.

"No. I am a Virtual Intelligence. While I can hold a conversation, I am not self-aware. I was merely designed help organic users with the purpose of processing and accessing data. Research on Artificial Intelligence was banned by the Prothean Empire after the Metacon War." Decadence explained. "In these archives, they key to interstellar travel is held. I am programmed to facilitate the adaptation of this technology into human designs... And to warn you of an incoming threat."

"A threat?"

"Most data about them has been corrupted… Organic input will be needed to attempt to decode and obtain information about this threat… From what remains, information about the threat is labelled under the name 'Reapers'."

Avatar System, Systems Alliance, 2257, April 1st

The name of the frontier colony in the system was Pandora, an Earth-like moon orbiting a gas giant. It was called like this by the captain who discovered it, the man himself was a snob obsessed with ancient movies nobody cared about at this point, so he named it after a vaguely similar planet from a personal favourite of his. Some vid called "Avatar".

Originally, this would have been like any other frontier world, quiet and steadily growing. But the discovery of a new Mass Relay had put everybody on standby as they prepared to open it.

Pandora… Such a fitting name for the current situation, if one knew the legend about Pandora's Box (It was actually a jar… But that is beside the point). Pandora was given a container, she was told not to open it. In it one could find all the ills that would fall upon mankind, she in her endless curiosity didn't listen to what the Gods had told her and freed all evil upon the Human world…

Ever since the discovery of the archives in 2030 and the formation of the now-defunct United Nations Space Agency (UNSA), humanity had been spreading recklessly through space. Opening any Mass Relay they found without any regard. This has lead them to find intelligent alien life, in the form of two pre-spaceflight species which had been uplifted, annexed and turned into "Associate Species" of humanity.

There was no hiding to the fact. Every time the Alliance entered a new relay, there was this danger of finding another interstellar civilization. One equal or superior in technology to humanity, which wouldn't necessarily have to be friendly. This was a fear that baffled many scientists, but didn't deter the pioneers who demanded more and more relays to be opened in order to get away of the Core Worlds.

"Commander Rynkor, a pleasure to meet you." Captain James Shepard of the ASV Prometheus, one of the Alliance's Gerald-class Frigates extended his hand to greet the massive figure which was wearing Alliance colours. It was alien, of course, having four pairs of eyes and teeth that looked as if they could maul over anything that crossed their way. Pretty average for a Yahg, really.

The Yahg readily took James' hand, while giving him and toothy smile that would intimidate anybody who was not used to dealing with the species in question. "The pleasure is mine, Captain Shepard! You have a hell of a career record, pretty good job you did against those pirates five years ago."

"The same goes to you, Commander. I heard you… Bit off the head of some human-trafficker?" James asked, as the two men started walking in the street towards a shuttle which was a few hundred meters away.

Rynkor cringed at the memory. "Yes… I was being shot at, and my mind just went blank for a second. I got to say, human taste is disgusting." He chuckled.

They finally reached the shuttle and boarded it as if it was any other day, oblivious of what was about to happen, preparations had to be made for the opening of this Mass Relay.

A few hours later…

"Where are we now?" Captain James Shepard asked, greeted by the sight of another system. There was a garden world in front of him. "That will be an interesting prospect for colonization once we go back home."

"There's yet another Mass Relay in this system." Navigator Tasar Sarmaer, a young-looking Raloi, told him. The Raloi were a bipedal, fully sapient avian species coming from Turvess. Much to humanity's amusements, they looked like Parrots.

"Get us in, plot an in-system FTL jump." Just as Shepard gave the order, the Eezo drive charged and they reappeared in front of the relay after a mild shaking. "Standard procedure, activate the Relay."

Dalo's Might, Batarian Cruiser

"What are these fools trying to do!?" Balak demanded at the Asari slave who stood before him, she just bowed and gave him the datapad with the readings.

"Master, the reports show that this fledging species seeks to activate the Mass Relay…"

Balak just signalled the Asari to walk away, to which she quickly and fearfully complied. The Batarian Admiral thoughtfully stared at the datapad, reading it several times over.

"Orders? We cannot let them open the Relay, another Rachni threat may fall upon the galaxy!"

This got the Admiral out of his thoughts, instead just sitting back on his chair. "That is true. Fleet, fire at will, perhaps they will become good, obedient slaves once we are done."

This was a golden opportunity. This mission, which had merely started as yet another scouting mission for colonization, could turn into much more than that. The conquest of a species, using its world, people and resources to make them subservient to the Batarians. He smiled at the thought of a potential implications of him being the one to bring this new species to fold, perhaps a bright political career would follow.

As the mass accelerator rounds hit the pathetic frigate, it tried to escape back to the Mass Relay which had probably brought them in.

"Let them go, and track them. I want to know exactly where they came from." Balak ordered, and the small fleet of four cruisers and 8 frigates stopped in unison.

Codex Updated: The Yahg Annexation

In the year 2100, the United Nations Space Agency (UNSA) discovered a pre-spaceflight species which was going through the advancement of a mid-to-late 20th-century civilization, they were called the "Yahg" and inhabited a garden world they dubbed Parnack. Rather than immediately initiate first contact, the government of the United Nations classified the discovery and created a task force to assess potential threats for human existence. The name of this top-secret international organization was "Cerberus".

Cerberus, shortly after its creation, was quickly given the assignment of studying and determining the potential threat Yahg posed for continued human existence, if they ever developed spaceflight abilities. Luckily for Humanity, and unluckily for the Yahg, an event would turn the tables to the United Nations' favour.

In the 4th of November, 2105, the Yahg bombed their own planet with nuclear fire. In the following months, hundreds of millions died through war, riots, radiation, nuclear winter, famine and other evils. The UNSA patiently waited as they gathered a large fleet at the orbit of Parnack and finally initiated first contact, already having an upper advantage due to the knowledge they had acquired about the species over five years and Parnack's state.

Yahg culture itself operates in an idea of pack mentality, in which a group of Yahg will refuse to cooperate until a leader establishes themselves through either brute force, political or social maneuvering. Once they did, though, they shown an astounding loyalty to their leader. Not holding a grudge, and finally cooperating. Cerberus predicted that attempting a peaceful contact as equals and friends would be disastrous.

The UNSA, aware of Yahg nature thanks to Cerberus' studies, went in on a display of force through Parnack. In a matter of days, all important industrial, military and economic centres were captured by the Human Military. The leaders of all Yahg nations were gathered and given two options: Either join humanity as an Associate Species, or be left to perish.

The Yahg, seeing how they had no hope of defeating a military centuries ahead in advancement, yielded. As soon as they did, though, terraforming stations were quickly placed to clean Parnack's atmosphere and hunger issues were taken care of.

The UNSA's decisions had very mixed reactions, ranging from praising due to saving a dying species and eliminating a future potential rival to riots on the streets opposing "Human Imperialism".

Parnack's nation-states were dissolved, a sole government was placed to serve as the planetary administration which would answer to the UNSA, as other colonial governments did.

In the coming years, Yahg culture, literature, art and science would be revolutionized thanks to their new human benefactors. The people of Parnack had been spared from extinction.

Codex Updated: Raloi Integration

In the year 2125 an UNSA scout stumbled upon a bipedal species of avian people inhabiting their Homeworld named Turvess. This species in question had the term "Raloi" to refer to themselves. The scout ship witnessed from a safe distance as the species launched its first satellite.

Once again, Cerberus went to work for several years on the study of this species and discerning whether or not they were a potential threat and determining how would first contact come to occur.

Gladly, this was much more peaceful than the situation with the Yahg. The United Nations of Earth sent a delegation, in order to greet the new species and "offer" to give them the key to interstellar travel if they became an Associate species of humanity. This process took a decade of intense negotiations and treaties, but eventually the Raloi acquiesced, noting human insistence and the vast difference in the military capabilities.

Reactions on Earth were more positive than the last time, and the diplomats were praised for their ability to negotiate without such a direct display of brute force as it occurred in Parnack. Years later, the Raloi would to go through a renaissance much as the Yahg were doing.

Codex Updated: The United Nations Space Agency

Now defunct, the United Nations Space Agency (UNSA for short), was the organization which handled human colonization, exploration and military efforts in the stars. It was founded in the year 2035, shortly after the United States' discovery on Mars and lasted for over a century until the year 2157.

The organization is noted for its efforts in safeguarding humanity's place on the stars during its early stages of exploration. It was the UNSA which lobbied for the founding of Cerberus, and went on with the annexation of the Raloi and Yahg peoples into Mankind's Stellar Empire to prevent any future competitors in colonization.

From the start, the organization was riddled with contradictions. The colonies it settled were not governed by locals, but rather by unelected governors sent from Earth. This would sow the seeds for rebellion, as many colonies seceded in what would be known as the disastrous "Frontier War" (2143-2157).

The war would be brutal from the start, and the UNSA's reactions on putting down the revolts just as harsh. In the last few years, as all colonies were about to be pacified, rebel ships were able to attack the Sol System. Even though they were quickly dealt with by the defence force, a mass accelerator round was able to escape from the enemy ships…

It, accidentally, hit Earth… Right on the Yellowstone volcano.

The chaos that ensued on Terra would scar it forever. Tension between the planet's nation-states rose to the point of nuclear war. In an ironic turn of events, Earth would have the same fate as Parnack did. The UNSA military would have to come down and force a military occupation in the planet. Then emergency re-terraformation would have to ensue.

The Frontier War was won, at a steep price. All leaders of the UNSA would be court martialed and dishonorably discharged. The United Nations Space Agency, even though making great contributions to Humankind, was considered to have gone rogue. It was promptly dissolved.

A new government body was made, calling itself the "Systems Alliance", all planets within it were given a parliament vote and the ability to elect their local assemblies. Their peoples' votes would also counted when electing positions such as the Chairman of the Systems Alliance, leader of all of Humanity and her Associate Species. The UNSA Military was abolished, then reorganized into the Alliance Military.

Earth was now under full control of the Alliance, like any other colony world. It was decided that nation-states in it would be ended as they posed a risk to stability within human space. Instead, the "Terran Assembly" would be created as Earth's local government (Which would operate in a manner much similar to any other of the Alliance's Colonies).

A/N:

This story was done with one purpose in mind: Trying to explain the Alliance's role in the galaxy during the game. This is because, by sheer numbers and common sense, a species like Humanity wouldn't be expected to have much of a say in galactic politics, much less gain enough economic and military power to challenge the fourth most powerful species in Citadel Space (The Batarians) so quickly.

The function of this story will be to strengthen humanity in order to make this possible, to justify its primordial role in galactic politics during the Reaper Saga.

This time, the Council won't establish contact with a small species barely into colonization… But with a large Multi-Species Empire with two centuries of experience in space travel and an extensive Military (Not enough to rival a council species… For now. But definitively comparable to the Hegemony in its size). And when the Reapers attack Earth, they will find out that attacking the homeworld won't be such a crippling move against the Alliance as it was in the canon (Partly because of the extensive colonization of other worlds, and partly because the Frontier War lead to quite a decline on Earth's population...)

That said… There will be other changes I want to make to this universe, first contact with the Batarians rather than Turians was one of them. You shall see.