User blog comment:The Milkman/The Writing of the Ending/@comment-24174486-20120726200543/@comment-99.240.73.6-20120822113854

"Also, its rule in the story was not foreshadowed enough."

You're told that in order to use the Crucible, you need the Catalyst. What does the Catalyst do? Help you use the Crucible. It fulfills the role in concluding the story that you were always told it would; the only thing you didn't expect was that it was an AI behind the Reapers. Its revelations and the reason it created the Reapers doesn't change what you were told about the Catalyst or what you ultimately do.