After finishing the last episode, I'll sum up the philosophical issues as follows:
Lelouch is the type of character who is driven towards being a meticulous tactician. He must, if he wants to protect what is dear to him. The object he originally wishes to protect is his dear sister. To secure her future and exact revenge against the emperor, Lelouch wages war with the empire. The power of one man is limited, so he comes to rely on the help of others to meet his goals. Through his power of Geass, this leads to the use of ultimate manipulation. Initial questions are, "Does the end justify the means," and, "when do you venture too far in trying to protect what is dear to you?"
Through the first part of this anime those are the big questions. Lelouche manipulates the hearts and minds of everyone at his disposal to achieve his goals. He dawns the mask of zero to gain the support of those who feel oppressed, and rally them against a common enemy. His goals are two faced. He wishes for the freedom of japan, but is completely secondary to his desire to secure a good future for his sister.
As things get more complicated, his goals change, and his methods of achieving them become further steeped in bloodshed and deceit. He is a cold and calculating person, but not without emotions. He casts off his emotions to meet his goals. Yet, he still cannot remove himself from his attachments to others, the instinctual drive to relate to other people through friendship. Though almost every relationship he develops becomes subject to manipulation toward his own desires, he still cares for some of the people closest to him who lend him all their faith and trust. Yet through his methods, he comes to lose them all, either through death or new found hatred.
Lelouch fights with tactics above all. The only chains that bind the will of people and their ability to achieve their goals are the constraints of morality we willfully put upon ourselves. This anime displays one thing as strong as anything else. Good and evil, right and wrong, just and unjust: none of these are as black and white as they may seem. The track that Lelouch follows above all is that the end justifies the means. Assuredly, the more he lost on the way, the less he had to lose, the looser his moral restraints became, and the greater his power grew. With everyone within the field of his trust at his disposal, his will to do whatever it took to win, and with a mind that was truly masterful at discerning the nature of people and the future they could create, he became a great force of vengeance. Equally great was his ability to attract the forces he needed and the support of all those oppressed by the empire.
Yet he was not invulnerable. He was checkmated many times by numerous enemies, the the most dominant of them being his father. The emperor sought to "rid the world of lies." In essence, his end plan was to disintegrate the barriers between the minds and hearts of people, to eliminate the ego, and thereby destroy the nature of the reality we live in. To remove the separation of one mind from another is to merge consciousness into the pure collective. It is the antithesis of the nature of this world, a world where people are individuals with their own choices and the ability to make their own determinations on what is right or wrong. Though mankind's nature is to hide his ugliness behind the mask of his ego (his individual self), it is through the act of this guise that he is truly able to learn and to interact in a reality that belongs to the individual, based on his/her own thoughts and actions. To take that away is to eliminate the extraordinary level of free will that exists in this destitute state. Though the ugliness we create may lead us into war, hatred, and dishonesty with each other, these perceived "negative" aspects to human nature are necessary for free will as we know it.
As I would've done, Lelouch rejected such a reality devoid of the individual self. Charles wanted a world frozen in time, Lelouch wanted a future of mankind's own choosing. Upon the defeat of Charles, the question was no longer about whether or not to eliminate the human nature that binds us all to war and discord. The struggle once again came to how we can circumnavigate our ingrained constitution of behavior, and continue to exist in peace.
Schneizel wanted to subjugate humanity through fear. By using massively destructive weapons, he sought to be the greatest power which nobody could oppose. With him, peace would be assured through the bondage of trepidation; a de facto peace which cannot last. Any force that has the power to subdue the violent nature of humanity is only effective as long as it is the dominant force. Should the rebellious nature of man rise again, it would create another force even greater, and the cycle of war would start anew with power far more immense.
Lelouch also rejected this reality. Having nothing left, and abandoning all ties and all obstacles that stood near or far to his heart, he pledged to move forward in securing the only future he saw fit. A future where people decide for themselves how they wish to act. A future where their anger and hatred is concentrated upon one figure just as their hopes and dreams had been once before through the mask of Zero. the future he chose was a future that extends into eternity, a future that allows for man to develop without the constraints of fear and subjugation.
He took on the role of a supreme monarch, and used his power to reshape the world, cast out all his enemies, and in doing so, focus all the hatred of the world upon him, even those he held dear. Upon his victory over all his enemies, the world was united once again under his supreme rule. Yet, a world ruled by a monarch is not a free world, not for the people under its rule. In his final act, without even the slightest flinch or sign of weakness, without a word spent for pity, forgiveness, or to seek the understanding of his plight, as Lelouch had always done, he took full responsibility for everything he wrought upon the world, his family, and his friends. He took the full weight of his sins, his burdens, and the hatred of the world and took it all with him to his grave; a final atonement. And with his death, the world was positioned to move forward, united and free of divisive hatred. He lost everything he cared about and his life. He was given the opportunity many times to stop and hold on to what he had, to stop and accept the state of the world, to accept the return of those he had always fought for and who were miraculously *revived, but never did he waver. In the end, for him, the means were justified. In the end, he carried that weight for all of humanity without so much as a hint of strain. Such was the act he put on from under the mask...