Lore-friendly Headcanons You Use and Why? OBVIOUS SPOILERS!

A few non-ending lore-friendly headcanons:

1) Reaper harvesting does not involve reducing a species down to goop, pumping it into a Reaper shell, and somehow absorbing the species 'essence' from that goop. It involves reducing a species down to its nervous systems, using those nervous systems as circuits and processors within the Reaper shell, and indoctrinating the consciousness of each person trapped within their harvested brain.

It's dark and a bit gruesome as headcanons go, but it explains how the Reapers seem to contain the minds of the people they harvested when melting a person would not preserve the mind. It also doesn't actually contradict anything that we see in ME2 - it just contradicts the interpretations that Shepard and co are putting on what they see.

2) Shepard spent the period between ME2 and ME3 advising the Alliance on the Reaper threat, and being taken seriously (by Anderson and Hackett, at the very least). Being under lockdown was just the cover story to placate the Batarians and the Council. This one actually explains how omni-tool heavy melees are available at the start of the game, when the codex states they were developed as a response to the Reaper invasion (although you can alternatively interpret the codex as saying that omni-tool heavy melees were developed as a response to husks, which had already existed prior to ME3).

3) The Leviathans kept the Crucible designs from being wiped out. This is mostly just to explain how the Reapers could be so efficient at wiping out previous cultures, yet the Crucible designs consistently failed to get wiped out, even when actual knowledge of the Reapers' existence would be lost. Devices like Liara's were probably also used to keep the designs in circulation from one cycle to the next, but the Leviathans are a good candidate for being able to preserve the designs when all other methods fail, and for being able to quietly return the designs into circulation without being noticed.

ME1:
- Captain Hannah Shepard rescued a little girl from Mindoir. The girl later later emancipated from her surviving family and adopted her savior's name and a new identity to enlist.
- Cerberus was already studying Shepard after Akuze. They experimented on resurrecting a brain-dead corporal with the intention to create a perfect expendable soldier.
- Wrex lived through the krogan rebellion and is as old as the matriarchs.
- Joker have a massive crush on FemShep and completely hate Kaidan
- Chakwas and Hackett used to be in a relationship together
- Thorian was alive through Shiala and the colonist was protecting her.
- Liara is an agent for the Asari Republic who are assigned to eliminate any threat to the Asari Matriachs including infiltrating Shepard's team. Her virginal bright-eyed innocent personality is just a cover for the cold and calculating person underneath.
- Conrad Verner is the president of Shepard's extranet fanclub

ME2
- There's a real headless corpse somewhere in Lazarus Station, Cerberus merely transplanted Shepard's brain onto a new semi-cloned and synthetic body. No matter how much you can try to convince me of Bioware's Space Magic, there's no way anyone could save that piece of charcoal.
- TIM was behind the malfunction initially perpetrated by Wilson.
- Liara's assignment by the Asari Matriach was to eliminate Shadow Broker and to gain its resources for the Asari's interest especially to protect a certain Matriarch who was being blackmailed by the original Shadow Broker for her damning relationship with Illusive Man.
- Chakwas was a spy for Hackett and Anderson to infiltrate Cerberus' Lazarus Project
- Tali and Reegar were lovers.
- The turian girl who Garrus sleep with was Nyreen Kandros. She left turian military and went to Omega to find him and hook up with Aria instead
- Miranda's preoccupation with being the perfect woman was due to the fact that she isn't one, genetically.
- Kelly's super perky personality is a lie. She is a Cerberus loyalist who suffered existential crisis after nearly being killed by collector nanites.
- The Janitor is also a Cerberus loyalist assassin. Why wouldn't they be, come on, the group are apparently expert at infiltrating, looking harmless until they kill you from behind.
- VS saved Shepard in Arrival DLC. Everything that occur after waking up is just a cover up to protect Alliance involvement in the destruction of Bahak system. Shepard regain Alliance trust by assuming the entire blame and stopping a potential war with the batarian hegemony.


ME3
- Nightmare kid was Shepard's dead son. She was pregnant before she died over Alchera and she's having hallucinations. Told ya, Shepard suffered postpartum depression since ME2.
- Jack and her Grissom's kids is Kaidan's J-Squad under his biotic special ops program.
- Garrus is the turian-equivalent of a royalty. Kinda explain the midlife crisis and his savior complex.... and the turian populace seem to grovel at him.
- Grunt went back to the planet where Okeer left his clones and recruit them into his Aralakh team
- Wrex and Eve had history prior to Sur'kesh rescue (oh I love pairing everyone)
-The "Lawson will find away" in Shepard's reconstruction project is the notorious mad scientist Henry Lawson.
- Bailey and Aria traced Anderson and Shepard's signal to the Citadel tower. Dr Michel found Shepard barely alive but kept her in stasis until rescue arrives.
- Alenko Sr was found alive but in hiding among the rebel group in Alaska and was reunited with his wife.
- Admiral Anderson was interred among thousands of Alliance soldiers who lost their life in the Battle of London. Kahlee visit his grave each time she came by
- Some of the geth programs survived inside young quarian's suits, whether they will regain their sentience is debatable. Admiral Xen began her secret project to resurrect them back into physical platforms. Within a decade or so, young quarians no longer need their suits to survive.
- EDI's consciousness were uploaded through the deep space and she woke up in her own flesh surrounded by her Cylons siblings.
- Reaper corpses are now free of its indoctrinating ability and its technology can be extracted. Repairing Citadel and Mass relay took time but not impossible.
- Humanity hold the custody of Citadel over London and allied together with Turian and the Krogan. Asari and Salarian dominance on the galaxy are severely weakened and Citadel council are now open to represent every species as it should be. Plans were made to create more space station in neutral territory to keep galactic peace even among the Terminus system.
- Admiral Tali'zorah and Primarch Vakarian eloped after years of service to their people.
- Due to genophage cure, the krogan populace are now vulnerable to disease and aging process but a shorter lifespan was considered a good trade-off as more Krogan children were born. Wrex and Eve die of natural causes a century after being together, leaving behind their first born daughter Mordin who are later mated to Urdnot Grunt.
- Shepard was kept in stasis for a few years of which she was able to undergo a secondary reconstruction to replace broken synthetic implant. Shepard could no longer hold a gun or walk without assistance, she left the Alliance and the Spectres. A small ceremony was held over Mindoir's orbital space station where in she happily became a Mrs Alenko to Admiral Alenko and she finally abandon the name Shepard.
- Joker found the remains of his home on Tiptree and became a recluse. He never found what happened to his sister.