Ok, this is my theory.
The pill form of the AI is the first version of the matrix, hence the blue emblem. It was imperfectly made by its creator. We never, ever, see the creator of the matrix in the movies. In fact, we know that the movie is the third version of the matrix from inception and hasn't been updated since. We know that the matrix reinvents itself after each cycle. We also know that the original two matrices existed in the real world conjoined to the false world. We know the original creator made it as a place without human suffering.
So in short, the 100 is the begining of all this. My prediction is that, to beat Allie 1, who struck first and destroyed the world, answers the question who shot first from the movies, and by the way, the 100 will use the second matrix. Once in the second matrix, the "commander" will inform clarke that the AI is linked to the whole planet via the internet and solar panels.
Unfortunately, the second matrix is not a perfect place either. In the second attack, the 100 and grounders use AI 2 to launch ancient weapons to block the sky. This was all part of AI1 plan all along as her conciousness will merge with the commander's when it finally is upgraded. With both the sentient and computer based AIs in Matrix 2, it becomes unstable, exposing the first 'Neo', and showing the one now known as the gate keeper and creator the flaw with the first two matrices. That humans die without suffering and the AI will die without humans.
The show ends with the first humans being put into battery pods as well as a few select people who refuse the first pill being imprisoned (so to speak) in Zion by the AI. The matrix itself then utilizes 'latent memory' to rebuild civilization in a light where humans exist eternally at the point prior to the AI being created.
Ultimately, the two become symbiotic and one not being able to live without the other. This show is or easily can be used to explain all the things the Matrix movies never did. Hence why the second AI looks like the tracker they pull out of Neo. Now Neo is the residual conciousness of all the previous human commanders that never desired for humanity to be stuck in such a limbo. The agents on the other hand are the first 'chipped' people from the first matrix who are now completely part of the matrix.
Hence why agents can take anyone's body at will-- only if they are submissive just like Allie, saying how she can't get past 'free will'. Neo, Morpheus, and Trinity are in fact the central feature continued out forever, because Morpheus is the reemergence of the human Version of the Chancellors; Trinity the commanders of the 100; and Neo the commanders of grounder nation. The mountain men are the last members of the people from the Mad Max films.
So my theory is as such. Mad Max series is the prequel, Matrix Series the finale, and The 100 to give the whole thing a linking storyline from apocalypse to eternal life. The Mad Max link is easier to see, blood-bags in mount weather, reapers made by the blood-bag leadership, radiated soil and massive wastelands. Also Charlize Theron's charcter at the end easily can be seen as the first leader of the grounders after the banishment of the mutated mountain men relatives.