Yeah the story is completely messed up. Almost half of the story missions talk about the AI Rasputin which is in the locked Jovian Complex that will be just later released in the expansion pack. The original story that was revealed on Reddit seems so much better than the "story" we have now.
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Indeed It feels like they kept the introducing parts of Destiny's story, like you said about the first few missions talking about Rasputin and then later took the rest of that story out to be sold in DLC. It's a shame Bungie have gone this low.