There is a debate that since AUTO worked under a hidden directive there would be no need for the probe ships to be sent to space. The Axiom actually functioned under the orders of the main CPU (voiced by Sigourney Weaver) under the Captain's supervision. AUTO was an assistant captain. The secret A113 command did not actually register until AUTO scans EVE inside the bridge. The green lighted beacon on the Captain's control panel signifying the positive probe was operated by the Computer and not AUTO. After the A113 was activated AUTO managed to take full control of the ship since the CEO authorized the special override. Essentially the female-voiced computer and AUTO were under two different competitive protocols. In the finale the computer is the one who gathers the entire crew to the Lido Deck. When the captain ultimately deactivates AUTO, the primary protocol prevails and the Axiom's CPU reroutes the coordinates of the ship easily.

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