I haven't played 2K6, but loved Crisis City in Generations.
Also, I have a theory that 2K6's internal retcon is what created the Time Eater in the first place. When its events were wiped from history, they spun off into another dimension where they gradually faded away, leaving the Whitespace around one last fragment of reality- Crisis City. The Time Eater is a gestalt formed of all the people who faded away.
It thus allowed itself to be captured by Robotnik, as part of a plan to draw Sonic and parts of the real world into the Whitespace, restoring Sonic's memories and allowing the remnants of the 2K6 timeline to return to reality with the rest.
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"I'm Commander Shepard, and you're standing in the biggest library in Citadel Space. Look me up."