Most confusing moments plot-wise for you?
I'm sure there were quite a bunch of them.
"You're from the 60s! Peace love dope! Back, back to the 60s! No place for you in the future!"
Hm, nothing. I mean, there were some mysteries and complexities, but the ending wrapped up things nicely. One of the best games ever!
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pre·ten·tious: characterized by assumption of dignity or importance.