Alex Mercer. All that time spent discovering the truth, being a boss, and defeating the virus... but yet here comes the second game that doesn't really at all explain his motivations and why it is that he went back on everything he worked to do.
Just... Wow.
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Miranda in Halo 3... God, she could've been such a great character to keep around. Plus I didn't like the way she died, just a Spiker to the back was so harsh and sudden.