Yup, it was - as has been expertly stated already - Cloud's true identity trying to help him overcome Jenova's influence.

Some people say that Cloud's actually a weak character and not a good hero at all, because his strength and self-identity came from the Jenova cells within him, and the illusions that were built up in his mind.

However, the fact that Cloud's real identity survived shows that he's got a heck of a lot of courage and determination that's all his own. With help, he was able to shake off the bonds and delusions and re-assert who he really was. And even after going through all that, he continued to fight rather than breaking down and wallowing in self-pity.
THAT is Cloud's real strength, I believe. Fighting for what's right even after his own world was turned upside down and inside out, even after he learned the truth and found that it was even worse than reality.