X-Men: God Loves, Man Kills
X-Men's insistence that its heroes are allegory for oppressed and misunderstood always faced the uphill battle of making us fear for the side with the guy who shoots lasers from his eyes. Most X-Men stories don't make the trek, but "God Loves, Man Kills" is an exception. Its red herring plot points frustrate (take a shot every time it pulls a death fakeout to get bombed fast), but its central villain is among the more intimidating foes in Marvel comics history. He's a bible-thumping hatemonger with a silver tongue and deep pockets; this motherfucker could be President if he wanted.
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