Protoculture Effect by Cyclone is a Mass Effect crossover/fusion with the Robotech saga:About a century after the events of Robotech: The Shadow Chronicles, humanity discovers the mass relay hidden in Charon and develops eezo-based technology. After the Relay War (it's a little late for First Contact, after all), the Citadel Council finds itself with an entire bloc of allied alien species to deal with, with the United Earth Alliance sitting in the middle.The story from there follows the story of Commander John Shepard, the first human Spectre, as he tracks down the rogue Spectre Saren.Can be read at Spacebattles or Fanfiction.net A spin-off, called Blue and Red: Stories from Shanxi, is an in-universe documentary about the Relay War. A copy of the codex is available here and is periodically updated along with the story.
Sadly, the codex was taken down from Fanfiction.net, but entries are still put into the chapters of the main story.
Alternate Universe: The presence of robotechnology and the Sentinel Alliance adds quite a few major and minor background changes, such as the batarians still having an embassy on the Citadel (the Council took their side on the Skyllian Verge this time around), and the quarians having friendlier port options in Sentinel space.
Also, the introduction of the Sentinel Alliance's potent robotechnology has inspired massive advances in weaponry from nearly every race. For example, the asari have learned how to make particle rifles similar to the ones Javik uses in Mass Effect 3, while the batarians have created a reflex-cannon-esque plasma gun and have unlocked weapons secrets from the Leviathan of Dis, specifically Thanix weaponry.
Amicably Divorced: After an Accidental Marriage, Shepard and Hunter decided to break it off after four months (specifically waiting to spoil the betting pool on how long it would last).
Also, the veritechs (capable of turning into giant robots themselves), geth armatures, thresher maws, and (off screen) the volus (who now use mecha as part of their armed forces).
In their attack on Terra Nova, the batarians have brought their own mecha.
Awesome Personnel Carrier: The Mako is even more badass with the addition of robotechnology. No, it doesn't transform (they already have two veritechs, so that would be redundant).
Bears Are Bad News: In the Relay War, this was definitely the case for the turians, who had to fight power armor equipped Karbarrans... who resemble upright, sentient bears. It's mentioned that their handheld guns are normally considered crew-mounted weapons.
Big Damn Heroes: Lampshaded; Jenkins says that Shepard was playing this role with Tali when he was picked up by the beacon.
Composite Character/Third Option Adaptation: Some of the possible background elements for Shepard in the game are given to Kaidan and Ashley. Kaidan, for example is the Sole Survivor from Akuze, while Ashley was Ruthless on Torfan.
Curb-Stomp Battle: The first fight between turian fighters and veritechs did not go well for the turians. Most battles in Blue and Red are told from both perspectives. The first fighter battle had to be all-human simply because there weren't any turian survivors.
"Don't get me wrong. They were good pilots; they knew how to fly. But when you're flying a fighter and using tactics all built on the same principles your enemy discarded as obsolete a century and a half ago, you're pretty much screwed."
Cutting Off The Branches: Subverts this for a lot of sidequests/choices or background details by having another party member take a shot at them.
Documentary Episode: Blue and Red is told primarily as a series of interviews between human and turian veterans of the Relay War, usually on opposite sides of the same battle(s).
Early-Bird Cameo: A number of characters who appeared in later games show up here. Most notably Jacob Taylor, Kasumi Goto and Legion .
Expy: Jane Hunter is a slightly transparent one for Fem!Shepard.
Fantastic Racism: Ashley is an... interesting case. She's suspicious of the Council races, like she was in canon... but she grew up in the Sentinel Alliance, which has such races as Garudans, invid, Karbarrans, Perytonians, and Tirolians. She even has Zentraedi blood in her. So she's not prejudiced against all aliens, per se... but she does hold the Citadel Races with a measure of caution, because while they gained the respect of the other races through combat (beating the Haydonites, the Zentraedi, the Robotech Masters, and the invid), the only time the Council and the Sentinels have gone to war, the end result was inconclusive and led to somewhat of a cold war between them.
On another hand, the Sentinels are, as a whole, very much not racist, as much of their strength came from working together. They even take in AI's, which allow an AI encountered in a very minor side quest in Mass Effect 1 to request asylum. Quarians, due to the similarity of their situation with how humanity once was in the Third Robotech War, also receive a lot of sympathy from them.
The Sentinel Alliance doesn't like the Citadel Council, though, for their handling of the Relay War. When the conflict was only between the humans and the turians, the Citadel (in the Alliance's eyes) did nothing to try to halt the war so long as the turians were "punishing an upstart race." But as soon as the rest of the Alliance took to the field in an invasion of a turian colony, the Citadel scrambled diplomats to try to secure a peace with this new interstellar coalition of species. This unfortunately gave the Citadel the appearance of a callous and uncaring group of bureaucrats to the Sentinels and is one of the reasons for the Cold War between them.
Fix Fic: Used sparingly. The main difference so far is Corporal Jenkins surviving the drone ambush in the game's first mission specifically because he's wearing a Cyclone this time around.
For Want of a Nail: The Sentinels didn't have much experience with mass effect technology before meeting the Citadel, which some people questioned, as the Prothean ruins on Mars are a matter of record in canon... except that the ruins were, in this timeline, under Mars Base Sara, which was destroyed in the First Robotech War by Lisa Hayes, obliterating the ruins. Yes, that means the plans for the Crucible, too.
Frickin' Laser Beams: Handheld laser weapons and laser carbines are available... but at the same time, the story notes that they can be finicky, require a lot of calibration, and that up-armoring soldiers reduces laser weapons' effectiveness, despite their ability to ignore kinetic barrier shielding.
The finickiness is only in regards to a particular weapon that is still in use as a marksman rifle because it has good range and power, and amazing accuracy when properly calibrated. So when a certain turian acquires one, the following line should not come as a surprise to anyone:
Garrus: "Garrus to all points. I love this rifle. That is all."
Half-Human Hybrid: Ashley Williams is known as the Butcher of Torfan in this timeline, and a very good soldier. This makes a lot more sense when you learn that she has both the blood of Zentraedi and Praxians in her veins (Zentraedi being genetically programmed for war, and Praxians being essentially a race of Space Amazons).
Shepard is one-quarter invid on his grandmother's side.
It's mentioned that the Zentraedi are so absorbed by humanity that many humans have at least some Zentraedi blood in them.
Word of God is that Shepard could have children with aliens if he embraces the invid side of his heritage.
Heel-Face Turn: The invid are full members of the Sentinel Alliance by the time of the story.
Humongous Mecha: This being is a Robotech crossover, the Normandy also carries a pair of veritech fighters as well as the Mako.
Recent chapters have revealed that the Citadel is trying to copy various mecha. So far, the most noteworthy addition on that front are the Predator P powered armor (non-transformable turian armor made to be an answer to Cyclones), a volus military unit that relies on their own three meter tall mecha (which given the size of volus, is pretty big for them), and both turian and batarian Walking Tanks.
Interspecies Romance: "Boney von Richthofen," an extremely talented turian pilot who was among the first to shoot down a veritech, eventually settled down with a veritech pilot (This being Robotech, of course it was the pilot she had a rivalry with during the Relay War). Note that "Boney" is not her real name, but is instead a nickname given to her by her enemies, as a shout out to the World War One fighter ace "The Red Baron."
Loophole Abuse: The UEA clearly notes that the Treaty of Farixen's restrictions on dreadnoughts is based on mass accelerator cannon yield. It has nothing to do with the ships' actual size (of their carriers, for example) nor does it mention reflex cannons. The Council lets them get away with it in exchange for getting the rest of the Sentinels to agree with certain other restrictions in the Citadel Conventions.
Mythology Gag: Garrus recognizes the female turian heading security at a facility on one mission:
Garrus: "I have reach, but... she has flexibility."
Garrus finds a laser rifle which can ignore kinetic barriers, has decent power, and superb accuracy... as long as it is properly calibrated. And it needs lots of calibration.
Also, Ashley punched a certain reporter.
The armor that the asari use (when in service to Matriarch Benezia) is described as using "compressed diamond" as part of its armor composition, which indicates Silaris armor (one of the upgrades you could get for the Normandy SR-2 in Mass Effect 2).
The particle beam rifles that those same asari use are clearly based on Prothean particle beam rifles, such as the ones you get once you recruit Javik in Mass Effect 3.
Number Two: Lieutenant Commander Jane Hunter, descendant of Rick and Lisa and an old Academy friend of Shepard's.
Oh Crap: Double Subversion when the turian forces attacked a hill on Shanxi and ran into a pair of antique Tomahawk destroids (that's Warhammers to you BattleTech fans, only with even more guns and missiles). First, they got scared, then they started laughing, then the destroids opened fire and the laughter quickly ended.
Original Character: Kilika, a batarian Special Intervention Unit operative assigned to Shepard's command. Not a Mary Sue.
Powered Armor: The Citadel Council started developing armor of their own after the Cyclones show up. Garrus gets a suit so he doesn't feel underprotected.
He is seen later trying to add missile launchers to it. It's unknown if he succeeded or not.
Right for the Wrong Reasons: Slightly averted with Operation Nutcracker, an operation undertaken during the Relay War (the equivalent of the First Contact War in canon). The Sentinels discovered that a planet in turian space (Telos) had massive orbital refueling complexes and was being used as a waypoint that turian fleets could use to get to Shanxi. Operation Nutcracker involved going there and blowing up those stations to prevent fleets from hitting Shanxi. It worked... except that while, yes, the turian fleet did use Telos as a stopping point, it was so that they could discharge their FTL drives in the magnetosphere of the planet, not so that they could refuel (the complexes were just an afterthought). So while the planet was an important stopping point, it was not for the reason the Sentinels thought, and Telos continued to be used for the rest of the war.
Rock Beats Laser: Surprisingly averted for a Mass Effect crossover, which have a tendency to make the Citadel much weaker. By Word of God, the Citadel and the Sentinels are about even, tech-wise, with both sides having advantages over the other (The Sentinels have the advantage in energy weapons and FTL, while the Citadel has a far more extensive knowledge of element zero technology, and so on).
Ship Tease: Leaning heavily towards Shepard/Tali already (she's known Shepard since before the events of the game now, so they've already had time to grow on each other), and maybe Hunter/Kaidan.
The previously-mentioned planet Telos with its massive orbital refueling complexes.
Space Cold War: Much like Renegade, the Citadel and Sentinel Alliance don't always see eye to eye. The UEA sometimes acts as a mediator between the two, but even they sometimes engage in acts geared towards wooing certain races over to the Alliance's side.
Some of the effects are already apparent: Batarians have developed a form of reflex cannon-esque weapon in addition to reverse-engineered Thanix-esque weapons gained from the Leviathan of Dis, the asari have new biotic armor as well as Prothean particle weapons, the volus have their own mecha platoons, and the major Council races have all started to adopt new ship designs and philosophies.
Spared by the Adaptation: Nirali Bhatia, Jenkins, and the AI who was siphoning money from Quasar machines in Mass Effect 1 (Shepard granted it asylum).
The Stations of the Canon: Often averted where possible. Especially regarding when and where certain characters get introduced (ex.: both Tali and Jacob are on board the Normandy at the beginning).
Interestingly, some of these events have both been averted and played straight. For example, Nirali Bhatia, a minor character whose only existence was as a minor plot point in a small sidequest in Mass Effect 1, not only survives Eden Prime, but joins up with the crew. Unfortunately, she does die later in the timeline, by being ripped apart by the slaves of the Thorian.
Another example: In canon, a turian named Tonn Actus had a set of Wrex's ancestral armor. In this story, he had it... but was forced to sell it to cover expenses. He sold it to Donovan Hock, an antagonist of Kasumi Goto, DLC squad member for Mass Effect 2.
Suspiciously Similar Substitute: Hunter for Fem!Shep. There was also a third friend of the two named James Farmer. Shepard is Colonist/War Hero, Hunter is Spacer/Ruthless (as is Ashley), Farmer was Earthborn/sadly not Sole Survivor (that's Kaidan).
There Is No Kill Like Overkill: Kaidan uses allof his veritech's missiles against a thresher maw. Somewhat justified because even in canon, they are very hard to kill and take a lot of punishment. That justification, however, is lessened because the maw could not have stood up to one of those missiles, let alone all of them. Zig-zagged, though, because Kaidan has the "Sole Survivor" background, and has some issues regarding thresher maws and how they killed off his unit.
Throw 'Em to the Wolves: Shepard gets Wrex's ancestral armor back by meeting Hock alone, introducing him to Wrex, then leaving to go about his business.
Tron Lines: The armor that Benezia wears (said to be the asari answer to Cyclones) have these.
Wave Motion Gun: The Sentinel Alliance uses this as a loophole in the Treaty of Farixen; the treaty's terms limiting the construction of dreadnoughts only limit firepower based on mass accelerator weapons, not on the extremely powerful reflex cannons.
The batarians have recently created a reflex-cannon-esque weapon for one of their ships. The Sentinel Alliance is not pleased, even though it only has about one-third the power of one of their reflex weapons, and is a far greater power hog.