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Tear Jerker: Operation Flashpoint
Cold War Crisis
Near the end of the campaign, Guba loses his temper and shoots his secretary. The character in question might have been scheming and manipulative, but you still feel sorry for the brutal murder. The event marks not just Guba's final Moral Event Horizon, but the definite start of his Villainous Breakdown as well.
The many deaths of Resistance's main characters. When you finally reach the Bittersweet Ending of the campaign, at least half of them have been Killed Off for Real. Including Troska's girlfriend and Troska himself - he does a Heroic Sacrifice in the final mission, so his countrymen could live to see another day.
Made all the more depressing when you realize that Guba managed to get off the island on time and escaped justice scott-free (justifiedPlot Armor, since he needs to show up in Cold War Crisis and Red Hammer). So, in a way, The Bad Guy Wins. On the bright side, the tiny island nation is saved and it's hinted at that it gained protection from NATO and peace from the Soviets after the war.