NOTE: This is JUST A THEORY! A GAAAAAME THEORY! I'm not proclaim this as 100% truth, okay?

(+also, if @ShadedSunrose , or any other person who related to FNaS games will read this, I would be glad if you will finally answer my question)

So, what if Golden Sonic we see in FNaS 1-2, is actually just Shadow Sonic/Eggman, possessing Origin's body? What if after Nightmare Golden Sonic completely melted away, & became Shadow Sonic, his original plan after time travelling to 1991 was just to make himself a hew body, replace Origin Sonic in the timeline, & prevent "The Bite of '91"?

Let me get it straight:

After arriving to the past, he came just in time when Sonic & Tails were about to make "Golden Sonic"(Origin Sonic, to be exact). He then possessed the cloning machine, or cloning material inside it, & started messing with Tails' settings, wanting to created a new physical body for himself. Possibly, due to both of Tails AND Shadow's settings for Origin's AI were mixed up, THAT was the cause for an error that created Origin we know today. Shadow's plan was successed.....well, partially, as due to getting fully physical body, & not being a ghost anymore, he completely lost all of his powers—he's now just mortal being like others. No teleporation, no time travelling, nothing.

But there was one even MORE epic fail in this plan—as his settings were mixed with what Tails already typed for Origin Sonic's AI, Shadow.....didn't actually replaced him. You see, as we know from FNaS 4, & may assume from FNaS 2 & 3, machine CAN mess with clone's mind by redacting their AI settings, & even if the clone you making is possessed by a ghost, the ghost's mind can ALSO be "redacted" & altered by your clone's AI(example is Nightmare clones—even despite Phantoms DID possessed their new bodies, they still were turned into monsters, due to N.G.Sonic was tampering their AI). So yeah, Tails literally just "redacted" Shadow Sonic, altering his mind & erasing all of his Dr. Eggman's memories—now, he just identify himself as "Golden Sonic, who entertains children", nothing more.

But at the same time, it doesn't mean that Shadow Sonic COMPLETELY gone! More like his true entity was just trapped in this walking talking living "prison", as Origin's body started to melt & decay, Shadow started to slowly "awakening" from this eternal stasis. Was you ever wondering, "why Origin Sonic already have a sort of paranormal abilities, like causing glitches for electronics, if he's not even Golden Sonic yet?"? Well, maybe thats just a reflection of how Origin's body becames weaker & weaker to keep holding Shadow Sonic's spirit inside, so as long as he keep melting, more & more of his supernatural abilities will start to coming back, until his body will completely melt into black inky puddle, & Shadow will be completely released.

Also you may wonder "even if Origin sees us as the robber who need to be stopped, why is he so violent & just kills us?". The reason is almost the same—unfortunately, Origin Sonic we know & love is literally just dying inside, as long as he keeps melting, he not only feels unimaginable pain from this, that slowly drive him insane, but also his mind is literally just slowly fading away, until he will completely "fall asleep" & die, as long as his own mind keeps fading, Shadow Sonic not only slowly tries to get out of this "prison he accidentally created for himself", but also slowly takes more & more control over Origin's body(+partially, the rest of Origin's mind), with not only his powers, but Eggman's memories also returning as well. And as the nights progress, Origin starts to identify himself more & more as Dr. Eggman, than actually himself, with all his insanity & bloodlust, along with Origin's own craziness & pain, only increasing. Probably, he even started to realize that nightguard he was attacking......is actually just him from the past, & in order to at least somehow end his sufferings, he caused "The Bite of '91", hoping that Eggman we were playing will die, & he will begone as well.

Then, after Origin was left to rot, locked in the basement for 24 years, he probably tried at least something to prevent his death & complete madness, so as Eggman's general intelligence & knowing about how to use cloning machine were returned to him, he tried to recycle & "repair himself". As we can see in RockClones, he tried to hold himself from that for at least 9 years, as in 2000, according to how '00 Golden Sonic look in RockClones easter egg & one of the CloneChannel's arts, he look more or less the same as Origin, besides his eyes are red, like '15 Golden in FNaS 1 has, & his cloning material, that leaking from them, is glitching. Then, he finally decided to recover himself—it saved him from fully melting, & Origin's mind was a bit regenerated, meaning that he became less insane at least, & less Shadow Sonic(with all his powers being gone for a while). But Golden still needed to save the cloning material inside of machine as much as possible, & wasting it wisely, or at some point he'll ran out of it. Probably, THATS why his shoes, tophat & bowtie are changing their colours throughout the series—he just barely even know how to properly use the cloning machine, & after recycling & recovering his body it makes some....errors to say at least.

And it was only 9 years from 24 he needed to survive, until he'll be found & sent to FNaS 1 location. Origin & Shadow both were still inside of it, but at the moment of 2015, when he was found, he probably had only around 10% of still being the same Origin, while 90% of him was Shadow Sonic. Yeah, he still couldn't remember his name, couldn't remember his original plan, & even couldn't remember his origin & what he is, still identifying himself as Origin, but unlike his '91 self, '15 Golden already was unphysical enough to being able to teleport whenever he wants, despite his body was also already weak enough to just not being able to normally do anything by his own limbs(thats why Golden Sonic can't walk or even stand up—his legs just too weak for that). The same thing was for '17 Golden from FNaS 2—he was probably only around 5% Origin Sonic, & 95% Shadow Sonic, & probably wasted so much material on recovering his body before, that he just wasted it the whole machine's tank. His body is now melted to the point that he can literally messing with people's minds, making them seeing hallucinations, & probably even making the nightguards(Amy Rose, for example) keep returning to their job, like some strange feeling just forces them to coming back until he & his bew friends he got can finally kill them. He can also literally morph his own body in anything, including even transforming into giant floating head.

But the end of this madness was happened somewhere between FNaS 2 & 3, when Golden(Origin) was so tired of all this pain & crazyness, & maybe even from murdering people, that he decided to just peacefully give up on surviving, & let Shadow Sonic inside of him finally release from his body. As it happened, Golden Sonic lost all his insanity, but at the same time, he lost all his powers, including even power to still keep living—now he is just a desolated husk, who is like a disabled person on a verge of life & death, can do absolutely nothing, besides just accepting his fate & decay completely, until he will lose his consiousness, & turn into a mindless puddle he should have became back then. The rest of the story ya know by yourself—Golden Sonic's soul died completely, until Dr. Eggman's spirit just possessed it & turned into '27 Golden Sonic we know in FNaS 3(leading then to future creation of Shadow Sonic in the first place), while Shadow Sonic, after being released from that body & leaving Origin to die, finally got all his memories & powers back, so in order to not fall in the same mistake, he decided to revise his plan, & instead just became friends with all of his past selfs(Origin Sonic, 15' Golden Sonic, '17 Golden Sonic, '27 Golden Sonic, & Nightmare Golden Sonic), & used them all to do what we see in FNaS 5, & finally kill Eggman(who is also their past self) for real, in order to break the time loop.

Also note about Dr. Golden—despite Origin was "dead", his soul didn't just release to heaven like other clones did. Technically, he still was there, inside of his melting corpse, just unconcious & eternally "sleeping" with almost no way to awake him. But once Dr. Golden made his new body, he recovered not only it, but partially Origin's mind & soul too—the only problem was that THIS time, AI settings for that new body was not mixed up, so Eggman was fully in control over his body this time(Origin, on the other hand, was just trapped inside of this body, just like Shadow Sonic was trapped inside of him). And after RockClones team could finally put an end to Dr. Golden's madness, & Eggman's spirit left the body completely, Origin's recovered soul was still there, & as now there's no one blocking him, he finally could take a normal control, & live a happy long life with his new friends