Eventually, his friends convince him that they’ll make sure he doesn’t do anything that would harm anyone and they go looking for Aerith. When they arrive at the Forgotten Capital, they find her praying—she’s summoning Holy to stop the Meteor from crashing down into the Planet. But, when Cloud begins to approach her he loses control of his body once again, he nearly slices Aerith, but his friends call out to him and snap him out of it—another example of him exerting a free will that he apparently shouldn’t have. When this happens he sees Sephiroth, the very evil in the world, come down from above and stab Aerith right in the back. This created one, if not the, most touching moment from me in a videogame. All of a sudden, I shared Cloud’s hatred of Sephiroth. I was hit hard with Aerith’s death, as was Cloud, and things suddenly began to change.
Cloud: “...Shut up. The cycle of nature and your stupid plan don't mean a thing. Aerith is gone. Aerith will no longer talk, no longer laugh, cry... or get angry... What about us... what are WE supposed to do? What about my pain? My fingers are tingling. My mouth is dry. My eyes are burning!”
Someone who had deeply cared for was suddenly taken away by the person he despised most. From this point on, Cloud would be very different. He would soon stop doubting himself, stop any control from Sephiroth/Jenova, and put an end to all this mess by defeating Sephiroth himself.
A little later on, Cloud eventually falls into the Lifestream and suffers a severe case of Mako Poisoning, as noted by the Doctor of Mideel. But there’s a very specific key here, the Doctor clearly states that no normal person could have dreamed of surviving this much Mako exposure. Cloud, however, is not a normal human being. He had been exposed to Mako once before and had been injected with Jenova Cells. But this trip through the Lifestream did something… different. It completed Phase III of the experiment conducted by Hojo. Cloud was exposed to an extreme amount of Mako, which is what the third Phase consists of, and because of such Cloud is able to have his incomplete cells become complete. From here, neither Jenova nor Sephiroth is capable of exerting a controlling force over Cloud. The control they could once exert over him is gone, vanished. The explanation as to why is right there.
Doctor: “Mako poisoning...... Quite an advanced case...... It appears this young man's been exposed to a high level of Mako energy for a protracted period of time. He probably has no idea who or where he is now... Poor fellow, his voice doesn't even work. He is literally miles away from us. Some place far away where no one's ever been... All alone...
I'll say it again; he's got Mako poisoning. I've never seen a case this bad. An immerse amount of Mako-drenched knowledge was put into his brain all at once...... No normal human could survive it... It's a miracle he did!”
Within this same timeframe, Cloud, with the help of Tifa, also begins to piece back his past and attempt to overcome his inner demons. They go through many steps, many of which I covered, that describe the problems Cloud had as a child and what happened on that fateful day five years ago. This along with the exposure to Mako would allow Cloud to become the strongest, both mentally and physically, that he’s ever been. Sephiroth’s mind games would no longer affect him and Jenova attempting to exert a control over his body had also ceased.