Maybe it's version 2, or maybe version 3, but it's finally working pretty well. It's a complicated environment, difficult to track, so you keep throwing in slightly more advanced Agent programs to keep things organized for you. Each time the cycle runs through, you take the best that the system has produced, The One, and reuse some of its code in the next generation of AIs. The system is fast, running at the speed of the computers, so a hundred years passes for the AIs while you monitor the experiment and take notes. Occasionally prompting is needed, so your fellow researcher pulgs herself into the inner matrix as The Oracle to offer vague advice peppered with statements that seem prescient to the AIs, based as they are on The Oracle's knowledge of how the system is configured. Each time it works, and the AIs get a little smarter, a little more emotional, a little more like humans. You continually tweak the Agents, too, to make sure that they can keep the rest of the AIs in line.

Finally version 6 rolls around, and things are the best so far. The winnowing process has worked exceptionally well, producing an AI that shows particular promise. Your friend The Oracle has arranged the prophecies to set the right conditions for emotional responses, and she has planted doubt, and the AI performs marvelously, expressing what seems like it might be genuine love. As always at this point in the program, you're nervous as the time rolls around again, but the AI doesn't disappoint, resurrecting itself and demonstrating that it sees the matrix exactly for what it is, a completely artifical construct without limits.

Hm, that was unexpected. The One somehow invaded one of the Agent programs and destroyed it. Still, things are going smoothly, and with the sentinel programs heading toward Zion, everything is set. It's a complex environment, so the unusual behavior of the Agent program will surely work itself out. Other programs have wriggled out of the normal rules of operation before, but since none of them realize the full scope of the uber-matrix, they're kept mostly in line. As this cycle draws close to its close, again, you insert yourself into the matrix and offer the AI known as The One the same choice you've offered The One in each version of the matrix. You paint the choice he makes in the terms he would understand, calling them "humans" and so on, but maybe you give away a little too much. Perhaps you're not as used to thinking within the context of the matrix as you should be. In any case, he makes his choice which may not really be a choice (since it is result of his programming, could he have made another?). Are you disappoint by his choice? Was it the choice you expected? It's hard to tell, I guess we'll have to wait until the third movie to know for sure. You seemed dispassionate, which would be odd if as much was truly at stake as you told the "Neo" AI.