Headcanon Sonic/Knuckles storyverse

Alternate Universes/Zones
There are countless zones, countless versions of Mobius and the other worlds in the universe(s). There are so many that even the Zone Cops have found it impossible to discover and identify all of them, though they are working on it.
Some of these zones are wildly different from one another, others are so similar it can seem eerie.
Some differ in obvious things like the laws of physics, others in more subtle ways, the paths history might take given a single alteration in a choice someone makes.
In some worlds, events might play out that would have been impossible in any other, or history may take precisely the same paths in a different order, a different cause and effect.

Twilight Cage: flow of time
Time flows very oddly in and through the Twilight Cage, formerly known as the Twilight Zone—indeed, time may flow oddly within any zone when compared to the universe that one is familiar with.
The Nocturnus, for instance, found themselves transported to the Twilight Cage thousands of years ago, but experienced at most only a few years before finding a way to escape.
The Dark Legion, on the other hand, were exiled to the Cage hundreds of years ago and were trapped for a few generations.
Even those who are imprisoned within the cage together might experience a different flow of time from one another. For instance, a young Nocturnus woman who called herself Adi-Ra encountered a young Luger, who could have been her twin brother for their age, during one of the Legion's raids on the other colonies. Though she took refuge and remained with the Legion, she clearly did not experience time as they did; she remained that young woman as Luger grew up, and even his own children seemed older than she when Luger and Mari-Su were killed.
The Legion had once estimated that they passed only one year in the Cage for every four years that occurred within Mobius, and while this was often true, it was not consistent. Thus time could pass one year for one year during some events, and pass one year for eighty during others. A study of just why this happens has not yet been conducted.

Nocturnus Tribe
When the echidnas chose to distance themselves, early in their world's history, from those races they deemed too primitive and dangerous to associate with, they divided into two groups based on their ideals.
One faction found their way to the island they would eventually call Albion, there to conceal themselves from this world, develop their own civilization, and bask in their presumed superiority over the other races.
Another faction, the Nocturnus, elected to wander the world, to observe the other races — though out of respect for their brethren in Albion, most of this observation was done in secret — and to use what they learned in developing their own civilization. They, too, suffered from the notion that their technological superiority made them superior in other ways, and they were not immune to the ways of evil and tyranny.
With their exposure to the world, however, the Nocturnus realized that even their advanced technology was no guarantee of that superiority, and they decided that there were many paths to explore, including the martial arts and magic. It is believed that they were among the first to discover and develop magitek—a particular variety of magic that manipulates circuitry and electronic signals.
Many of the Nocturnus, after so many generations had passed, elected to give up wandering and relocate to their city of Nocturne. Others continued to explore, and to eventually interact with the very races they had been taught to shun.

Forgotten War
During the war between Albion's Knights of Aurora and the Order of Ixis, both sides used any weapon at their disposal, including the creation and control of several mutates, and the genetic manipulations that transformed the Mobian Tasmanian Devils into the beastly Devil Dogs.
These crimes against nature were only known to a select few, however, and most of Albion's citizens sought to end the war with their honor intact.
Those members of the Nocturnus who continued to wander found their way to Albion. Their ambassador, a particularly powerful technomage, offered his services to the city, to fight if they must, but mostly to help protect the civilians so that the fighters could be spared to the battle.

But it was not to be.
One of Albion's politicians saw the group's tribal lifestyle and the ambassador's magitek, and thought them primitive compared to Albion's more obvious technology; he was jealous of being shown up by what he saw as a poor imitation of his own superior breed.
He could not, however, deny the aid they provided, not directly. But after the ambassador had fallen in love with and wooed the councilor's daughter, the older echidna found his solution. The councilor visited Albion's fighters and civilians alike, and began whispering rumors, convincing the citizens that the Nocturnus were demons, no better than the Ixis threatening the city. Many of the fighters agreed to ambush and steal away the ambassador and the young woman, whom the councilor had claimed was demon-marked and corrupt, and send them to their deaths.

The ambassador and his lover survived, however, just long enough for the young woman to bear a son. That son grew to adulthood, eventually traveled to Albion with the remains of his pirate crew, agreed to protect his mother's homeland, took part in the war that was still going on, fell in love himself with the daughter of another political leader, and smuggled out her and the other intellectuals and such fighters as were needed to protect them.
These intellectuals traveled on to Downunda and ultimately founded the city of Echidnaopolis, while the warriors — those who called themselves the Knuckles Clan, and the remains and descendents of the ambassador's group of Nocturnus — temporarily separated to have their own adventures and conflicts.

Dark Legion Cybernetics and age
The Dark Legion's law has a certain minimum age requirement before any member is allowed to receive cybernetics, with the primary exception being for medical emergencies.
The reason is simply this: a child at a certain stage of development will continue to develop in spite of any modifications, and the cybernetics must be fitted precisely to the body for them to work properly. While they can be adjusted slightly to allow for growth spurts, or changes in weight due to health reasons, they must be replaced very soon after. Otherwise, the child can become crippled beyond even the cybernetics' ability to restore, or even die if the conflict between flesh and machine is severe enough.

Three possible exceptions to this rule, and four blatant violations of it, are known to exist.
Kragok and Lien-Da, as Grandmaster's children, had access to the best resources the Legion had to offer. Between that and their ruthlessness, they could easily afford to upgrade as much as they liked, even at the cost of denying these resources to the other members of the Legion.
Julie-Su had been given her cybernetics soon after her older siblings had had her mindwiped. However, as she was at the very low end of the acceptable age, this may not truly be an exception.
The technomage twins Tyson and Elys-Ia had had their voice boxes replaced as children, as punishment for some prank or other that they'd pulled on Moritori Rex. Their magitek alone enabled them to modify the cybernetics, to prevent internal damage as their natural bodies developed, but at the cost that they always sounded like their voice boxes had been "damaged." They never found a way to make their voices sound natural.
The Guardian Spectre had had cybernetics forced upon him at a young age by Moritori Rex, somewhat early during the Legionnaires' masquerade as Spectre's father Tobor. Spectre only remembers the incident in his nightmares, and nobody else among the Brotherhood has discovered the cybernetics, so how old he was when it happened is not known for certain... though he does vaguely recall Moritori's son Luger protesting that Spectre was "too young."
Kragok's daughter Aki-Ra (known at the time as Ama-Ye, the daughter of some other Legionnaire entirely) received cybernetics at an extremely young age under the guise of "medical emergency." Her cybernetics, however, were minimal in amount, and aesthetic in nature rather than intrusive. Kragok deemed that they would not interfere with her physical development, and had added them only as a way for him, and temporarily for Julie-Su, to keep track of the child.

On the other end of the age spectrum, most Legionnaires add to their cybernetics as they grow older.
This is not some aesthetic pleasure, an equivalent to people in our world who cover their bodies in tattoos or piercings.
Rather, this is a necessity, as replacing body parts with machine makes the rest of the natural body tend to fall apart more quickly.

Spectre's burns, pain, and Chaos Force
A third degree burn is one of the most damaging burns, one of the most life threatening burns there is...
And yet one of the kinds of damage it inflicts is to destroy nerve cells, resulting in the inability to feel pain from those burns, or indeed, to feel much of anything.
However, I'd written that Spectre, who I envision as having suffered this type of burn or worse, as being in constant pain to the point of needing those pain killers, no matter how much he is spooked by their less desirable side effects.
While I did not think too strongly on the matter when writing the story, I did recently develop an explanation that went along with what was already in the story. My theory, here, is that it is not his physical burns that pain him, but rather his connection to the Chaos Force. He had never been trained to access that force prior to his injuries, had instinctively plunged into it to protect himself from the flames... and now, quite literally, cannot live for very long without it. And yet, because the raw power within him reacts very oddly to the more refined power of the Chaos Emerald or the power used by his fellow Guardians, it is very difficult for anyone to train him, to teach him how to control that power so that he uses only enough to live and no more. Thus the very same power that keeps him alive flows through him constantly, burning him from the inside out.

Spectre... and Knuckles' fate
First is the matter of Locke's plan to mutate Knuckles within the egg.
The Brotherhood in general was mixed on whether the plan should be allowed. While the majority of those voted to allow it, for most of them it was less an approval and more a decision not to stand against it.
Spectre, for his part, was most definitely against it, though at the time, it was only intuition born of his own experiences with his barely controlled power, and the threat he could become — and had become on more than one occasion — to the people he cared about... and suspicions about what Kragok had done to Remington.
It is only later, far later, after Spectre encounters Aki-Ra and learns the extent of Kragok's experience that he realizes just how terrible Locke's plan could be if it went wrong.

Meanwhile, Spectre's feelings about the anti-Enerjak weapon could only be described as conflicted.
On the one hand, he knew that much of Enerjak's evil was a result of the power corrupting him and his perspective rather than true evil, and Spectre realized the nature of the weapon could just as easily be turned against him should the Brotherhood ever find themselves considering it. On the other, protecting their people as a whole was important....
Seeing that his "father" (as the weapon had been planned long before the impersonator was revealed) argued against the weapon's creation, Spectre was almost tempted to argue in favor of it, simply out of the habit of not trusting his father's judgment or morals. Ultimately, though, Spectre decided to hold his tongue regarding its creation, but urge that the Brotherhood try very hard to find a way to avoid needing it.

Luger
Luger was a more merciful sort of Legionnaire. His ambitions focused on protecting his people, and he had little stomach for war. With Moritori Rex for a father, however, he had no choice but to learn to be ruthless.
As such, he would be inclined to protect even his enemies, to prevent those like Spectre from becoming Moritori's tool... but he would not hesitate to use that same tool if he thought it necessary to protect himself or his ideals.