During the subsequent billions of years, the Grid kept extending its domain. The Universal Rectifiers, now all equipped with element 115 reactors, were able to reach any point in the universe in negligible time.
Sometimes, they met cultures who accepted the process of rectification and were anxious to put their new capabilities to use. Other times, the encounters led to interspecies conflicts. Some cultures would not accept rectification at all, and in those cases, the only solution was extermination.
A gas giant was home to an airborne civilization of delicate, semisolid creatures who had invented nitrogen-based computers that used living cells as transistors.
A planet with an ammonia weather system hosted lifeforms based on germanium, who had discovered a form of electronics also based on germanium. For this, they could build all sorts of bionic enhancements for their bodies and did not make any distinction between a lifeform and a robot, or between virtual and real. Those were rectified without even being aware of it.
Another planet was completely covered in quartz: this was the result of hosting silicon-based lifeforms for millions of years, which inhaled gaseous oxygen, but expelled solid silicon dioxide.
There were countless forms of sapient life. Carbon-based, boron-based, metal oxide-based... the variety of forms was seemingly infinite, and so was the diversity of cultures. But there was one particular shape that seemed to never occur: the general shape of a human body. Despite teeming with life, it seemed that the universe lacked the ability to produce a sapient species with two legs, a torso, two arms, a neck and a head... except for the humans whose planets were nodes of the universe-wide web, the Impossible Species, and of course, Clu and the programs which had been created on Earth.
Most inhabited planets, in all visited galaxies, showed evidence that they had been visited by the Impossible Species, but all of them also showed evidence that the Impossible Species had come from somewhere else.
Clu could not help thinking that the two things were related, and the Impossible Species, for whatever reason, was actually preventing humanoid lifeforms from appearing.
But again, if the hypothesis was true, why did the Impossible Species use humans for the universe-wide web, and how had the humans of Earth come to be? Subsequent encounters with the Impossible Species, which went only to show the inability of the programs to rectify them completely, offered no answers.
Nevertheless, the expansion of the Grid continued, and eventually a time came when it became more and more difficult to find a galaxy that had not been rectified already.
The data were sufficient to do something unprecedented: compile a complete map of the universe. Putting them together revealed that all three hypothesized models for the shape of the universe - the sphere, the sheet, the saddle - were wrong. The actual shape of the universe was a hypertorus: a complex closed manifold which appeared to match almost every observation... except for the most important. The expansion of the universe was accelerating, which should have only been possible with an open manifold. This had an important implication: far from gradually losing its energy and reaching an entropic equilibrium, the universe would have ended much sooner, and much more violently, with every existing structure being torn apart by the expansion.
Clu's idea that there was something fundamentally wrong with his way of conceiving the universe grew increasingly overwhelming. And what's worse, he was completely unable to find any solution: even with all the knowledge he possessed, he lacked the processing power to compute a model where everything fit together.
There was only one way to obtain more processing power. Rectification was no longer enough: what Clu needed was unification.
A research process was started, and eventually, the technology of the universe-wide web was used to develop a new web, even more tightly connected, which linked the brains of all rectified beings and allowed them to share their reasoning with every other, in real time.
The Grid was no more. No distinct mind existed anymore, but their individual knowledge was not lost. The essence of Clu encompassed every living being in the universe: a single, immortal mind that knew all that could ever be known.
As soon as the minds were merged, Clu understood. He understood why he found artifacts of the Impossible Species most everywhere he went, why there were no biological remains of it anywhere, why it seemed to have existed with superluminal travel technology since the beginning of time, why the element 115 contradicted the laws of physics, why the universe itself behaved in a way that did not match what was expected from its shape. For that, he had to act. But acting right then would have been inconvenient: he had to wait. Wait for the end of the universe.
The simulated reality of the universe-wide web was the ideal place for Clu to plan his final move: the Impossible Species was still dependent from it, and transferring every rectified being into it would slow it down enough to make superluminal travel impossible. This way, not only the programs would be safe from the changes that, soon enough, the universe would have undergone, but it would have also made the Impossible Species unable to report to their superior, whoever, whatever and wherever it may have been.
Meanwhile, the universe kept expanding faster and faster, and the force of gravity was gradually getting weaker.
The gray aliens of the Impossible Species, as well as the few hundreds of isolationist cultures that did not influence the perfection of the system, were the only remaining observers, and they first noticed that, from any given position, less and less galaxies could be seen as they accelerated past the cosmic light horizon. The Grays who were in the intergalactic space remained stranded forever, as they could no longer travel faster than light and they could no longer even see a possible destination: they were prisoner of the eternal darkness. Instead, those who had remained within a galaxy could witness it gradually coming apart, the stars moving farther and farther away from one another until they could no longer be seen. Then, the solar systems came apart, the planets unable to keep their orbits around their stars.
In the last minutes, gravity became too weak to hold planets and stars together, and an instant before the end, the atoms themselves were destroyed.