He reached Phase II and while he had the cells coursing throughout his body, they were still incomplete at best. This allowed for Sephiroth to easily manipulate and control Cloud—focusing on the problems of his past and cause him to lose control due to the incomplete cells in his body. In most circumstances, Sephiroth will have complete control over Cloud if he wishes. Only when Cloud is pushed up against a wall with nowhere to go can he actually exert his own will and control his body. Despite what many people wish to believe, this is NOT the product of a weak-minded individual. It, in fact, requires someone of serious mental ability to not break under the pressure like this. He is not like anyone else. While Hojo often refers to him as a “failed experiment” he is anything BUT that. Cloud exceeded every single one of Hojo’s expectations and therefore he is regarded as a failure. Hojo set out to create a SOLDIER that would emulate Sephiroth, but Cloud had clearly gone beyond that level the moment he had managed to live through with incomplete Jenova Cells in his body. Some of serious physical and mental endurance would have to be capable of doing such a thing… someone like Cloud Strife. Further, Hojo says himself that Cloud should NOT be able to exercise anything close to “free will.” The incomplete Jenova Cells in his body should allow for complete and utter control by the host—Sephiroth, or Jenova, if you prefer. Neither should have the slightest bit of trouble with them, but they do.
Hojo: “He's a Sephiroth clone I created after the real Sephiroth died five years ago. Jenova cells and Mako, with my knowledge and skills, have been combined with science and nature to bring him to life. ...I'm not wild about the failure part, but the Jenova Reunion Theory has now been proven. You see, even if Jenova's body is dismembered, it will eventually become one again. That's what is meant by Jenova's Reunion to start. Five years have passed, and now the Clones have begun to return. I thought the Clones would begin to gather at Midgar where Jenova is stored. But my predictions were not entirely correct. Jenova itself began to move away from the Shinra Building. But being a genius that I am, I soon figured it out. You see it was all Sephiroth's doing. Sephiroth is not just content to diffuse his will into the Lifestream; he wants to manipulate the Clones itself.”
Back to the subject at hand, after he had awoken from the dream of Aerith, he was quite frightened. She had left, but he did not want to pursue her. He was afraid of what might happen when he found her, he was afraid that he couldn’t control his body again, and he was afraid that it would all lead to him failing… failing his friends. Cloud constantly showed signs of fear throughout the game and this, I feel, is what made Cloud far more human than people give credit for. He was an extremely realistic character because of this. He was not the unwavering hero who stood for justice; in fact, many times he preferred not to pursue anything. These are all very human emotions. Cloud was not always willing to put his life on the line and he certainly didn’t want to do something that would mean him putting his friends in danger—in this case, they all traveling together. Things such as these are what really bring me to liking him and considering him so much better than every other videogame character out there. His realism is undeniable for scenes such as these.
Cloud: No… I'm afraid. If this keeps up, I may go crazy! I'm afraid…”