The origin of Pandora’s Box
Pure humans are incapable of channeling mystic energy. Thus, members of the Arcane Order are by definition part non-human (in fact, nearly every human by now is not "pure"). As humanity has become less pure, they have begun to lose their ability to interbreed with anything, making it more difficult to breed with more powerfully mystic races to produce "superior" offspring.
After the birth of the Caretaker, the Arcane Order learned the truth about humankind, their link to Emmanuel, and their "anti-mystic" nature. This revelation shocked the Order to its core, and it was decided that humans should be studied in great detail to better understand this phenomenon. The Order began to study them, and found a way to measure a human’s "purity." Those that were more pure had the bizarre potential to interbreed with other species more readily (their genome was optimized for adaption, particularly toward other mystic species).
The original members of Pandora’s Box (four of the exiles from the Arcane Order), were particularly interested in applying this phenomenon toward breeding superior mystic magic users. Unfortunately, due to the dilution problem described above, they found themselves in a bit of a bind. After being exiled for pushing their beliefs too aggressively, and expressing too much of a desire to get involved in world affairs (along with three other members of the Order), they turned to genetic research.
Thus, the original goal of Pandora’s Box was to create offspring that combined the human power of assimilation with the non-human power of mystic potential. The name derives from the idea that their release from the astral plane was the opening of a "Pandora’s Box" upon the world, and nothing would ever be the same.
The names of the Seven exiles are: Jendu Gryffindor, Tungoa Hufflepuff, Sai Ravenclaw and Vixlecais ("Vix") Slytherin, the four founding members of Pandora’s Box; Morgan & Aldan Huntington (Merlin’s parents); and Soren Corsair, their fearless leader. (Their last names were taken after their exile.) They went on to each play a role in World War III. Though they were all slain during the war, the descendents of Pandora’s Box (one male child of Jendu + Tungoa and one female child of Sai + Vix had a child who recruited others into the fold) continued the legacy, though after a few more generations the original message became somewhat confused.
Trenton’s birth
More recently, Pandora’s Box fell apart when Trenton’s parents (Felix and Madison), "pure human" subjects of cruel experimentation, fell in love, then rebelled against their masters, killing the head researcher and destroying all of the research. Some of the other test subjects, who were to be recipients of this work, were extremely angered by this turn of events, and swore revenge against Trenton’s parents. Madison’s recently conceived child, however, had been imbued with the organization’s final research attempt, based around an infusion of beholder DNA.
Felix and Madison kept a low profile for years, and raised Trenton to reject the values of their magic-loving former masters. They taught him that he had been created for the purpose of resealing magic, with the hope that his abilities would give him an edge toward this seemingly impossible goal.
Trenton’s ultimate power is not his eyes, but rather his ability to "biologically" tap into mystic energy and channel it, despite the fact that he is a "true human" capable of interbreeding with any other humanoid species.
His "pure human" nature coupled with the splicing of beholder DNA (offshoots of Emmanuel, possessing some pseudonatural traits) has enabled him to begin not merely countering magic, but inflicting backlash upon his enemies.
The sage on Percepi was a dwarf with an interest in the Obelisk that was destroyed to unseal magic. He became obsessed with how it worked – how his ancestors had constructed it – and began to reresearch it. His dislike of mystic magic fueled his efforts, and soon he had amassed quite a bit of knowledge about "Pandora’s Box," the legendary "container" artifact, and how it could be harnessed to reseal magic.
Felix and Madison found out about the sage’s work, but their irrational fear of magic prevents them from traveling out of the solar system (unless they were to use a conventional transport which would take years). In addition, they were still in hiding from the remaining members of Pandora’s Box. Thus, they sent Trenton out into the world to recover the information, and begin his quest.
Pandora’s Children and the Brotherhood
The other Pandora’s Box test subjects, left twisted and mutated but without the reformation of their genes being complete, formed the seed of what would become the "Brotherhood of Homo Sapiens Superior," led by Erik Lensherr.
Though many more would join the cause of the Brotherhood (as there were many who had dabbled in genetic experimentation and research, who shared the Brotherhood’s views), it was this core group of test subjects who also secretly belonged to Pandora’s Children, an anti-soulmech terrorist group dedicated to the integration of human and non-human DNA by any means necessary. Latching on to StratCo’s work on necrophagic techniques over two hundred years ago, they picked up the research, despite the fact it was ruled illegal during the Dresden Accord.
Since then, the Brotherhood has acquired members inside StratCo itself. In particular, Reginald Pipwhistle has discovered that the Fearful virus more easily stabilizes necrophagic grafts.
Older thoughts
Trenton’s powers are derived from the Fearful’s influence somehow. How much of him is really "human"? How are the Fearful related to Pandora’s Box? How much of what Trenton "knows" about his parents’ organization is really true?
Trenton is human, but a descendant of a community that lived as part of Fjell. The Fearful altered the mitochondria present in humans, integrating themselves with it. As Trenton develops his eye powers, the latent ability of his mitochondria is unleashed, lending him properties similar to those of the Fearful.
In a sense, Trenton is "pure" human, in that he is directly descended from the originally engineered human, Pandora, unpolluted by non-human DNA.
The Pandora’s Box organization has been around in some form since humans’ inception. They are instinctually opposed to mystic energy, due to their genetic programming, and therefore the existence of the organization makes sense.
The only reason Trenton can channel mystic energy is because of the experiments performed by other Pandora’s Box members a few generations ago.