A/N: First off, thanks for the reviews and reading, nice to know that you guys are giving this a chance. Few things as clarification/explanation, in case you don't want to head over to spacebattles:
1) I felt that warp influence had to be handwaved away, for ME elements to stand even a chance for evolving and having a day in the limelight. Planned post-ME3 timeline will fix that, restoring "proper" canon!40k conditions.
2) eldar had to be handwaved away for the time being, as I felt otherwise they would steamroll over the Reapers and ME canon (with tech like Talismans of Vaul and psychic powers), rendering any potential crossover totally moot. They are around, and planned endgame of the post-ME3 timeline of the story is to get them back to their canon!40k status as dominant galactic presence.
3) Necrons. Canon!40k necrons, which I consider mostly associated with the Deceiver and the Nightbringer are still asleep. The Void Dragon is on Mars, nursing a headache from the incident with the princess, the lance, and the knight. The Outsider is, well, in dark space ;) Their influence is, well - consider some parallels with a certain hypertech omnicidal ME faction.
4) Orks are around, but they don't have Waagh! energy in the usual amounts, so no Weirdboyz and extremely few Warbosses.
5) Chaos. The three Elder Warp Gods are around since the War in Heaven, but their influence and interest in the materium is minuscule for the time being, as there are extremely few psychics running around.
Codex – Timeline (excerpt)
59,000,000 BCE – Earliest findings of galaxy-wide starfaring civilization, in the form of similarly constructed black dolmens and bone-like arches scattered in numerous star systems. Speculated home regions of this civilization include the Shrike Abyssal and the Nubian Expanse.
40-20,000,000 BCE – Unknown spacefaring civilization flourishes on the planet Etamis. The planet is thought to have been bombarded from orbit by another species.
37,000,000 BCE – The Great Rift Valley is formed on the planet Klendagon.
2,700,000 BCE – Unknown civilization on Carcosa is wiped out, speculated to be caused by runaway greenhouse effect.
300,000 BCE (estimated) – Unknown civilization in the Zelene system is wiped out in an unknown cataclysm, likely war with another species.
125,000 BCE – Two precursor races (one of them is thought to be the inusannon) battle above the planet Eingana. The aftermath of the battle leaves Eingana littered with the debris of hundreds of starships, resulting in widespread eezo contamination on the planet.
68,000 BCE – Prothean civilization achieves spaceflight. Over the next millennia, their civilization expands, culminating in the building of the Citadel as the seat of their galactic government.
54,000 – First archeological evidence of primitive asari.
53,000 – First archeological evidence of primitive salarians.
48,000 BCE – Collapse of the Prothean civilization. Evidence suggests both internal and external conflicts.
44,000 BCE – Krogan civilization emerges on Tuchanka.
13,000 BCE – Turian civilization emerges on Palaven.
12,500 BCE - Human civilization emerges on Earth
1900 BCE – Collapse of the krogan civilization due to nuclear war. Tuchanka becomes an irradiated wasteland.
580 BCE – Asari discover the Citadel.
520 BCE – Salarians discover the Citadel.
500 BCE – 0 CE – Founding of the Citadel Council. Numerous other races are granted an embassy, but rulership of the Citadel Council rests firmly with the asari and salarians. Turian Unification Wars. Due to inability to communicate meaningfully, krork species declared dangerous, and Council races are allowed (even required) to cleanse their would-be colonies from krork infestation, wherever the warlike species is found.
1 CE – 300 CE – Rachni Wars. Aggressively expanding arachnoid species surges out from the galactic east from behind previously unused mass relays, overwhelming Citadel forces with superior numbers and coordination. Salarian scientists propose uplifting krogans specifically for the war, and future induction into the Council. Uplifted krogan manage to eradicate the Rachni. Krogan begin expanding from Tuchanka, first capitalizing on goodwill due to their efforts, later using intimidation and brute force.
700 CE – 800 CE – Krogan Rebellions. Defeated by inviting the turians to the Council as full voting members and deployment of the genophage. As a result, krogan population is cut back, krogan colonies are deported back to Tuchanka. Citadel Conventions established. Spectre Corps established.
1600 CE – First sightings of the Collectors.
1895 CE – Geth War. Creation of the Migrant Fleet.
2069 CE – First human colony on Luna established.
2100 CE – First human colony on Mars established.
2140 CE – First human tests with FTL propulsion. The prototype ship vanishes after passing Neptune and engaging its FTL drive.
2148 CE – Mars Archives discovered. Establishment of research centers on the Promethei Planum and Noctis Labyrinthus.
2149 CE – Discovery of Charon Relay. Systems Alliance charter established. Colonization efforts begin.
2157-2158 CE – First Contact War/Relay 314 incident. Turians overreact to human science team opening a mass relay. Events quickly escalate into a shooting war. Fleet and surface actions culminate on and around Shanxi. Despite the turians having advantageous orbital positions, General Williams refuses to surrender and his forces dig in, managing to stalemate the turian ground forces. The escalating orbital bombardments threaten the viability of the colony world itself. The conflict is ended due to asari and salarian diplomacy negotiating an uneasy truce between the Hierarchy and the Systems Alliance.
2160 CE - Systems Alliance biotic training starts, using the expertise and contacts provided by Conatix Industries.
2162 CE - Arcturus Station, the new seat of the Systems Alliance is completed and taken into use.
2163 CE - The Dis Incident between the Batarian Hegemony and a Citadel science team.
2164 CE - Sirta Foundation scientists lead by Professor Munir Yildirim create medigel. Pinnacle Station established. N-level training established.
2165 CE- 2170 CE - Humans start colonizing and terraforming numerous worlds, mainly in the Attican Traverse and the Skyllian Verge.
2170 CE - Raid on Mindoir. First large-scale slaver attack on a human colony. Despite efforts, explicit Batarian Hegemony involvement could not be proven. Human colonization efforts stalled, focus is shifted to improve defenses on existing worlds. Citadel Council declines overt assistance and does not formally censure the Hegemony.
2170 CE - 2176 CE - Constant, ever-increasing skirmishing between various pirate and mercenary groups (suspected to be funded by the Batarian Hegemony) and the Systems Alliance forces in the Skyllian Verge. Fighting culminates in the Skyllian Blitz and the Battle of Elysium, where Alliance space and ground forces led by 1st Lieutenant Irina Pavlichenko smash a large pirate/mercenary contingent.
2176 CE - 2178 CE - Anhur Rebellions. Pro-slavery Na'Hesit faction supported by Batarian Hegemony finally loses when a joint Blue Sun and Eclipse mercenary team under Zaeed Massani massacres much of their command structure and demolishes vital communication nodes. Batarian officials claim the mercenaries were supported by Alliance N-level special forces.
2177 CE - An Alliance special forces team is lost when investigating a silenced science station on Akuze. A single survivor reports both the team and the station personnel were massacred by the largest recorded thresher maw attack.
2178 CE - Alliance Intelligence manages to locate a large pirate army on the moon of Torfan. Alliance Fifth Fleet is deployed in full against the base, with orders to neutralize the threat by any means necessary. Admiral Steven Hackett's fleet destroys the pirate navy, then Major Edward Kyle's marines supported by three N7 task groups demolish groundside pirate forces. Kyle is wounded in action, and his replacement, 2nd Lieutenant Alexander Shepard uses chemical and nuclear weapons to cleanse the remaining pirate strongpoint, disregarding civilian casualties.
2180 CE - Human-turian joint naval cooperation agreement signed, research begins on creating a new shipclass.
2183 CE - Systems Alliance ambassador Donnel Udina manages to convince the Citadel Council to evaluate a human candidate for the Spectre corps. First joint human-turian vessel, SSV Normandy enters service.
Codex - First Contact War (Δ EYES ONLY)
2157 - Late June, a Systems Alliance science team including G. Rokobungi, S. Yi, and T. Weyland locates and starts the process of activating Relay 314. The science team was succesful, but the relay activation was noticed and investigated by a turian patrol fleet.
Ignoring standard Council protocols and disregarding the messages of the automated probes spotted by their sensors, the turian fleet commander opened fire on the human vessels, with only two cutters managing to disengage and flee.
The turians, tracking the FTL wake of the fleeing human ships, encounter elements of the Alliance Second Fleet stationed at the Shanxi-Theta relay. Data analysis shows that Commodore I. Rackham timed his opening salvo 1.5 seconds after transmitting a message to the turians demanding they stand down from pursuit and identify themselves.
The turian fleet was forced to retreat less than an hour into the engagement, as their kinetic barriers provided little resistance to the ship-based laser weaponry of the Alliance fleet. Commodore Rackham did not pursue and eliminate the turian fleet, for which decision he was later criticised and put on trial (acquitted).
For the next month, skirmishes erupted centering on the Shanxi-Theta relay, as turian patrols and reconnaisance vessels fought with the ships of the Second Fleet. Both sides were later formally rebuked for not pursuing non-military options at this point, opting instead to an ever-escalating armed conflict (see report on turians using the conflict as justification for concessions from the Council).
The conflict escalated in September when Desolas Arterius arrived with the Aephus Legion, including elements of the Armiger Legion. Using tactics relying heavily on superior maneuverability (see naval training manual on microjump calculations), the turian fleet managed to whittle away Commodore Rackham's task force, pushing him back towards Shanxi.
The actual Siege of Shanxi started three weeks later. The orbital installations and Task Force Rackham managed to deny turian orbital superiority over Shanxi, but could not prevent the turians from landing troops, including mechanized forces.
General J. Williams, the commander of the Shanxi Garrison attempted to destroy the turian troops at their landing site before they could properly reorganize and deploy. The attempt bought some time for Williams, mainly due to the fact that Desolas Arterius was wounded in action, but it cost General Williams a sizable part of his mobile forces.
Deprived of the possibility of a mobile warfare, General Williams decided to focus on defending the four primary arcologies of the planet, leaving the outlying settlements to their fate, gambling on the turians focusing their efforts on eliminating his forces. His rearguard, lead by Captain Tadius Ahern waged a successful guerilla campaign against Desolas' troops, slowing their advance long enough to finish setting up the defences of Shanxi-Primus through Shanxi-Quartus.
Desolas Arterius focused efforts on Shanxi-Tertius, as his intelligence reported that the human food production was centered there. A week of close-range artillery fire was needed to break into the arcology, where the defenders stalled the turians for 22 more days in pitched urban warfare, reducing the arcology itself to rubble.
Infuriated by the unexpectedly high losses, Desolas Arterius ordered his fleet elements to start orbital bombardment of human positions. Commodore Rackham's attempts at disrupting the turian efforts were repulsed, and in days, Shanxi-Secundus and Shanxi-Quartus were reduced to rubble, resulting in approximately 3.5 million casualties, most of them civilians (see documents on turian doctrine regarding the handling and determining of civilians in combat zones).
With loss of over 70% of orbital support, cut off from extra-system communications, and supplies stretched by the influx of refugees and survivors, General Williams ensured to make his final act memorable. He ordered Captain Ahern and a small mobile force to leave the arcology while his remaining forces staged diversionary attacks on the encircling turians. Ahern was supposed to lay low until the arrival of the relief forces, and, if safe, wage further guerilla warfare against the turians.
When Ahern reported the success of his brigade exfiltrating and losing the pursuing Armiger Legion forces, General Williams had the steadily weakened barriers dropped, inviting a full-scale turian attack, and invoked Fairfield Protocol on Shanxi-Primus. The resulting incursion wiped out the arcology along with over 90% of the surrounding turian army, forced the aliens to evacuate to avoid total losses when facing the incursion.
Commodore Rackham managed to end the incursion by having his fleet saturate the site with both laser batteries and bombardment from orbit, then when the incursion became unstable instead of contracting and dissipating, he steered his already damaged flagship on a collision course. The resulting tectonic movements and weather pattern changes claimed hundreds of thousands of lives on the planet.
Bitter irony, that two days later, asari diplomats arrived, representing the Council, offering reparations and terms for favorable peaceful settlement of the conflict.