Cog In The Machine will reveal Agent Phoenix to be a robot.
The Agent has near superhuman abilities of adaptability and ingenuity, and has survived the complete destruction of a space station and an island base, without a clear explanation as to how. When Cog In The Machine introduces a villainous scientist who's confirmed to have developed our psychic implants, and has the goal of replacing agents with robots, it raises the possibility we've been one of her original prototypes all along. This would poetically explain why we can't seem to stay dead: we never really lived.- The opening credits for the game make this even more likely. One scene shows us trapped in what looks like the assembly location for her robots. The lyrics at this point include the suspicious line "I've built better than you...I have made you before, I can take you apart." Then, one of the clamps rips out our "heart"- only it's not a human heart, looking more like a pulsing piece of crystal. Hmm...
- Though this isn't outright confirmed in the game, it's heavily implied. Both Prism and Zor use Insistent Terminology in calling Phoenix one of Prism's "creations." Though this very well could just be referring to the TK implant in the Agent's brain, "creation" is a very strong word for that.
John Juniper is still alive.
Sure, getting electrocuted and made to fall 32 stories seems like a sure death, but we never get confirmation of his fate after he falls. There's also never mention of a body being found. Besides, Agent Phoenix survived the same ordeal along with a blown up space station, and if that's anything to go by, is the thought of Juniper surviving his fall really that outlandish?- Jossed. Juniper isn't mentioned in the third game past a fly-by Call-Back in the very beginning of the game.
Kinesium is this universes version of Psitanium
Agent Phoenix is a clone of Dr. Zor
As stated above, IEYTD 3 has about an eyebrow-raising amount of evidence suggesting that Prism "created" Phoenix, but what if instead of a humanoid robot or something, Phoenix was a clone? There's also the fact that Zor's voice is heavily distorted, making it hard to tell if they're male or female...like how the player/Phoenix is treated. Also, there's a suspicious detail in the "Winter Break" level of 1 that says that the hat "fits well" and that Phoenix and Zor must have heads of similar size. Dr. Zor is a Challenge Seeker who's more interested in challenging Agent Phoenix than world domination.
In the second game, if the player fails to stop the nuclear launch, Zor sounds more disappointed than successful, and in the third game Roxana comments on how oddly inefficient and easily-subverted critical elements of Zor's machinery are... opening up the possibility that Zor deliberately leaves their schemes just open-ended enough for an Agency member like Agent Phoenix to foil them. Even Zor's comment about there being nothing in the Agency worth saving could suggest they abandoned the Agency because they had nothing to challenge them.As an aside, if Zor makes a physical appearance in a fourth game, it would be fitting if they were dressed in a red trenchcoat and matching hat.
The painting of the woman in the ski lodge is Dr. Zor
The opening song in the first game was sung by a feminine voice, and heavily implied to be sung by Dr. Zor. The subsequent games had the prominent villain sing the opening song in what's supposed to be their singing voice, so why would the first game be any different? Besides, what's an evil lair without artwork of yourself?