Did you know that when Myrna asks you if you are a synth, saying “no” makes you a dirty great liar? It’s all true! Probably. Spoiler warning: contains spoilers on Fallout 4 and its DLC, Far Harbour.
First off, we’ll start with the Far Harbour DLC character, DiMA. If you are not yet familiar with DiMA, he is a prototype synth that suggests that you, the player character, may also be a synth. He suggests that the reason behind this is that you have one specific memory from before you awoke in the cryogenic capsule (the day the bombs fell), but nothing else. No memories of your first kiss or anything like that. Just that one, single memory.
Secondly we have the fact that everyone in Vault 111 is dead after the second thawing, besides you. It could be that you were the one person there that had a strong enough body to survive, but I make Endurance my dump attribute most of the time so that hardly seems plausible. What makes more sense is that the Institute killed everyone else – including you – and put your synth body (made from Shaun’s DNA) in the cryogenic capsule so that you don’t question your surroundings when you are activated.
“you have one specific memory from before you awoke in the cryogenic capsule […] but nothing else.”
Then there’s the fact that you upgrade in sudden jumps – like software updates. You can heal using any blood pack you find, despite other people having to worry about their blood group (some Gunners tattoo it on their foreheads). You can eat corpses to heal and get no ill effects, while the Trappers on Far Harbour probably have some nasty prion diseases from doing the same. You also never get cancer, despite wandering into nuclear fallout zones, and treating addiction is as simple as having a Refreshing Drink.
The most damning piece of evidence, however, is VATS. VATS just shows up at the start of the game with no announcement, it’s just like “hey, you can shoot things in slow motion if you like”. And it’s not part of the Pip-Boy software – you can use it in Vault 111 before you get the Pip-Boy. I’ve tested it myself. Where does it come from, then? The Institute. In the Robotics lab, one of the terminals contains a description of a “unique project”, where a synth can be upgraded to perceive time as being slower than usual while detecting the percentage odds of hitting a target with a ballistic weapon. Like, come on, that’s a dead giveaway!
“VATS just shows up at the start of the game […] like “hey, you can shoot things in slow motion if you like””
So why would the Institute make you a synth? I’d suggest it’s to do with creating free will. The Institute is all about improving humanity – their motto is “Mankind, redefined”, and want to repopulate the world with more resilient humans. Many Institute scientists claim that the synths are biologically superior to humans, but not capable of free will. If you go ahead and destroy your creators, you prove yourself to have complete autonomy (a bit like The Talos Principle). Of a sample of Fallout 4 players on Reddit, 65% of these destroyed the Institute. 65% of these were an experimental success. After its destruction, it could well be that the Institute had a remote server that uploaded your personality to every Gen3 synth in the Commonwealth.
Of course, it’d be very easy to spot synths then. Just look for the people carrying silly amounts of duct tape.