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I've gained access to the Historia Crux, and for some gates, there's a "Close Gate" option. If I select it, a fancy animation occurs, but it's not clear what, exactly, it does.

What's the difference between a closed gate and an open gate?

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An open gate is one that you've found in-game and used a fragment to activate. Open gates save your progress as you roam about, and as you leave them to return to the Hisoria Crux.

Some portals have the close gate option. When you close a gate it resets all of the events and content there (other than collecting fragments and key items). This is so that you can re-play the area to make different story-altering live event choices. Those portals that do not have a close gate option don't have multiple story lines to choose from. You can still go back to collect missed items, but there's only one outcome from completing that time period.

This is what you're expected to do in order to experience each of the anomalies for a gate that has many of them. It is also how you earn the Anomalous trophy / achievement.

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  • This confused me too, but the primer in the Datalog explained it okay, but this makes more sense.
    – Neon1024
    Commented Feb 7, 2012 at 16:56
  • If this is the only reason then why when you close the gate to new bodhum 003AF do you then need to replay everything you've done all over? It's like starting a new game but with all your current monsters and stats. It must have sone other purpose. Maybe alternate endings or something
    – user19751
    Commented Feb 10, 2012 at 18:53
  • @pavel Yes, alternate endings are among the reasons for doing so. Without spoiling too much there are some boss fights you can re-do differently once you're stronger, which result in different (paradoxical) endings.
    – Yuck
    Commented Feb 10, 2012 at 20:27
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    I wanted to add that all portals have a close gate button once you collect their seals. Commented Feb 14, 2012 at 18:43