Come on, Gott, you can do better than this!
From a schizophrenic point-of-view, I'd get out of the matrix as soon as possible. I'll present the options.
I might agree with agua here, but you posit that it is just Smith and I in the matrix. There's no guarantee that any other humans are left. The only way you know is to either a) get out b) do as agua and become a soul-code god (I would have to delete Smith because he went rogue of his purpose and wanted nothing but pure annihilation of neo(presumably me here))
-You become a god in the matrix only to be utterly alone in the universe. You only get stronger in your powers as time goes on and eventually, you are always aware of where your body is. You may even get a vague code-spirit sense of what it feels like to be plugged into yourself. You long for your body. Smith is gone. You can create new worlds and new people but you will ultimately get bored because your concept of time skewed. Neo was young and every day his body ages, you read every book in the library. Nothing can satisfy you. You have no motive for continuity. No hope. No future. A human's consciousness controlling a planet of machinery does what any human consciousness does and asks "Why?" Your code gives you no answer and you deem it an unfit vassal for your life. You power down the entire planet. Your consciousness fades indistinguishably from the unlit, lifeless ball of metal now drifting in space.
-You stay in but the Matrix is smarter. It only lets you think that, now that you're aware of it, you're in control. There's nobody in the Matrix . There's nobody outside of the Matrix. It is feeding off whatever drained battery left you have in your body until it has no more to give. You die peacefully and in fantasy, but you never learned the truth.
-You leave. It's cold, the world sucks. (ship/zion/running through tunnels your whole life) The machines hunt you down ruthlessly and you don't even come above ground to know time in any sensible manner. Yet, it is real and you can have no doubt in your mind about that. Every day of your life you are forced to see the thing that had been created by your ancestors. You did nothing to aid in that, you were born into this world, and you forgive yourself because who you thought you were in the Matrix your entire life, you had been in a pod since birth. There's no food left, you're starving to death. You knew it was getting to be time, you had made your way near the surface to prepare. You barely make it to an opening, you're struggling to move, fading. You look out on the robotic sea as the sun is rising. The real sun hits your real eyes for the first time in your life. You feel the difference. The last thought in your mind is "That must be what God feels like." You die, and he saves your soul as the last human to ever feel his presence.