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In the third game in the series, Clarke builds the Codex because he thinks he needs to turn the Machine off. Then it is revealed to him that

the Machine was actually created to keep that freaky moon in stasis, and therefore must be kept on. So Danik overhears and takes the Codex so he can turn the Machine off. Along the way, Clarke regains possession of the Codex.

Why doesn’t he destroy it immediately?

  • Videogame logic and a set up for the Awakened DLC/potential future sequel. – Broots Waymb Aug 20 '15 at 13:37
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From the Wikipedia plot summary:

The duo then finds a video log from Serrano, who explains that with Codex, the Machine can either free the moon or destroy it.

Isaac likely wanted to keep it to activate the machine and destroy the moon and finish it rather than keeping it in stasis and risking it waking up in the future.

In-game, a likely supplemental reason is Isaac's growing insanity due to the marker (The "Turn it off" phrase we hear repeatedly through the game).

This, of course, is also subject to the game designers plan in regards to timing and story continuation (Awakened would not be possible if the Brother Moon was destroyed). But this is more of my own personal reasoning and not really an excuse for plot inconsistency.

  • I don't trust what Wikipedia says in this case because in the prologue, the general wipes the codex's memory as if that solves the problem. At this point the Machine is already partially on, which is why the moon is frozen. Then Clarke turns the Machine all the way on, it seems, so there seems to be nothing left to do. – MackTuesday Aug 20 '15 at 17:42
  • @MackTuesday, what does that have to do with your question? Yes, he wiped it, but the information is not gone (hence the whole "Rosetta" thing). And the Wikipedia entry is correct in saying Serrano mentions the codex can be used to destroy the moon. – Broots Waymb Aug 20 '15 at 17:45
  • Also, Clarke doesn't know Ellie is a hostage until he's already on an irreversible trajectory to the center. (This comment was ninja'd.) – MackTuesday Aug 20 '15 at 17:46
  • OK, that makes sense. Maybe the Machine wasn't fully on until the codex was used. But Danik shoves it in without altering it in any way. Maybe the codex was left in "turn off mode" the whole time, but Danik doesn't check it. I guess I'm dissecting it too much at this point. – MackTuesday Aug 20 '15 at 17:50
  • @MackTuesday, possibly dissecting too much :P. But I don't think you're wrong. A new codex could always be remade from Rosetta anyway. Isaac simply knew he had to permanently solve the problem by activating the machine in "destroy mode". I'll also remove the Ellie/hostage detail. Haven't played in a while but I'm pretty sure you're right. – Broots Waymb Aug 20 '15 at 17:57

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