I see the closest analog for this latter ability in MEGS as being Dimension Travel, with the cyber world being a set of dimensions that represent different systems.
The eventual results of this work are a new race of ISOs, and a new set of uses for the ability to move people and things between cyber and real worlds. As hinted at by Kevin Flynn in Tron: Legacy, the ISOs are the key to a whole new understanding of the universe. The form this takes is their ability to see, understand and manipulate matter and energy in digitized form within the cyber world.
This combined with the ability to take things created in the cyber world into the real world (the first example being Quorra) enables a whole new approach to medicine, scientific research, engineering, transportation and any number of other fields. As Kevin foresaw, this holds the promise for a new golden age of mankind.
I also think that the abilities of the ISOs translate to a level of super-science genius in the real world, although they don’t have the ability to directly see or manipulate matter while they’re in flesh and blood form.
They are naturally smarter than humans, on average, as well as being athletic and even artistic. In the world of Tron: Genesis, at least, Quorra is a great example of the potential of the ISOs in that she is essentially like Einstein, Bruce Lee, Leonardo DaVinci, General Patton and Katherine Hepburn all rolled into one.
She spends a lot of time learning about Earth history, culture and art, as well as keeping up her combat training and doing R&D work. She’s helped in this by the fact that time moves much more slowly in cyber worlds, so she can do a lot of research and study in very little time by shifting into “pocket cyber worlds” or “whiterooms” (ala the prep area / weapons locker in the Matrix). She also has an eidetic memory (Recall) and the ability to Interface with any computer system, even in the real world.
Her biggest weakness as a character is that she has a huge blind spot where the IOs are concerned, and that allows problems to develop. Big problems.
The first and most developed of the new ISOs is named Lux. He is a natural ISO wunderkind, much like Quorra, although with less experience and wisdom than Quorra, due to not being mentored by Kevin and Sam Flynn, being much younger and having spent even less time in the real world than Quorra.
However, more importantly, he is the first to develop and use matter and energy reshaping powers in the cyber world. This is something not all ISOs can do, and those who can are usually limited in how they can use it. But not Lux.
He is able to heal any wound, cure any sickness, remove any deformity, and even change the appearance of anyone in the cyber world (Damage Transference and Transform). He can also make people stronger, faster, tougher, and even smarter (Enchantment). When they go back to the real world, the change sticks – permanently. And finally, he can reshape matter and energy into objects and devices (Matter Manipulation) that can also be quantum teleported to the real world.
The limits of his abilities are only in whether the Quantum Teleporter can reconstruct the changes in the real world in a way that fits with the laws of physics. But some advances have been made, and continue to be made, to stretch those limits.
The potential exists to eventually remove them altogether at some point in the future. Lux also has eidetic memory, the interface ability, and is also a highly skilled fighter, scientist, inventor, doctor and artist like Quorra. He is the pinnacle of ISO evolution to date.
But all is not well. Edward Dillinger Jr., son of the original and appearing near the beginning of Tron: Legacy, is disgruntled, to say the least. He is jealous of being overshadowed by Sam, Quorra and the new ISOs. As a computer expert with little expertise or interest in physics, the Quantum Teleporter is beyond him, and it is the center of what ENCOM has become.
He still participates in the development of the systems, though, and that is where the trouble begins. He becomes a “friend” and confidant of Lux, who shares a dark secret: he worships Quorra, but more than that, he is passionately jealous of Sam Flynn and wishes to take his place. Sam and Quorra stayed “just friends” when they first came back from the system at the end of Tron: Legacy, but eventually their relationship became much more than that.
Lux wants to have all that Sam possesses: Quorra, wealth, fame and influence in the real world. But mostly Quorra.
The Dillinger plot
Lux is an ISO, and IOs have a natural sense of honor and obligation to help humans, who after all created them, if only indirectly. But they share digital DNA with CLU, and possess even more moral flexibility in their nature. They are in some ways more human than most human beings. And so it is that Dillinger is able to manipulate Lux into acting on his desires.
They work together to get Lux out of the home of the new IOs: the ENCOM ISO Compute Cloud, a supercomputing cluster set up just for them, which is conveniently connected to the Quantum Teleporter. They plunder all of the research Kevin, Sam, Quorra and other ENCOM scientists have done, and steal a spare Quantum Teleporter and other devices needed to build their own system and make diabolical use of this wondrous technology.
And so it is that Dillinger and Lux become the masterminds of an underground criminal and terrorist organization, the aims of which are overtly to master the use of the Quantum Teleporter and the breeding of “corrupted” ISOs to give them the power to conquer the world.
They also gain influence and wealth by using the abilities of Lux and other ISOs to provide medical, cosmetic and other services to the world’s decadent power elite. People will pay a very high price to cure the incurable, become young and beautiful again, and even for the promise of immortality through transhumanist application of the quantum teleportation and ISO/system technologies.
At the same time, Lux’s ultimate goals are simple: kill Sam Flynn and have Quorra join him, by any means necessary, as his queen (empress?) while he conquers the world and remakes it in his image as a “paradise” for corrupted ISOs, with a few humans left for amusement and slave labor.
And all this sets up the continuing battles of Sam, Quorra, the “good” new ISOs and the loyal factions of ENCOM vs. Dillinger, Lux and their organization. Cool tech, lots of action, very much a comic-book style version of the TRON universe as I see it.
Quorra, Sam and Lux have real-world versions of the suits, discs and vehicles from Tron: Legacy, most of which is written up as being Gadgets with overall R#s of 2 or 3 and a few extra-scifi abilities like Invisibility and Force Field with Catastrophic Burnout.
I freely admit to taking wholesale inspiration from Robotech, the Legion of Super-Heroes volume 4 “Five Years Later” storyline and numerous other science fiction series and comic books for this plot. Please feel free to gently punch giant holes in it, and if you’re a Tron fanboy hopefully I have serviced you adequately (you know what I mean).