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United Federation of Planets
- The destruction of the old Earth Spacedock. The old one had been there for three years and to see it pulverized by the Undine...
Klingon Defense Force
- The entire tragic story of K'mtar's life a.k.a Alexander Rozhenko who was a diplomat from the Federation and tried to get the Great Houses to work together against threats. This got him thrown in Rura Penthe along with his suspicions of the House of Torg. Ultimately, it's clear no one takes him seriously in the Klingon Empire and even his own father Worf considers him a joke. It's not until he sacrifices his own life and is proven right in all of his suspicions that he earns his father's respect.
- The death of Martok's grandson at the bat'leth tournament. You crossed the entire Beta Quadrant and fought through legions of House Torg soldiers only to fail to protect him. It gets worse at his funeral as he died as a warrior but lost all of his potential. The fact Martok never even got to know his grandson when he comes back doubles the tragedy.
- While technically an All-Factions mission the discovery Martok has been alive this entire time and drugged for decades is both a Heartwarming moment as well as a horrifying one. Everything Martok has worked for all these years has been destroyed by J'mpok and his grandson perished in a cowardly assassination.
- Most of the Romulan Captain's story arc. It starts off with your colony being invaded and it gets worse from there. The penultimate mission shows that just about everyone abducted was or is in the process of being turned into more Elachi.
- 'Cloaked Intentions', the Featured Episode series focusing on the Romulans and Remans, has a couple of doozies.
- In 'Mine Enemy', a Romulan miner talks about her life and the destruction of Romulus:
"My family and I have been here all of our lives. It's a hard life, but it is all I know.
My mother used to tell me tales of the homeworld. She'd talk about the plazas in Rateg, or vacations she spent with her father on the shores of the Apnex Sea. And she would tell me about my father, who gave up his place in the military evacuation ship so she could live. He ... he never knew he had a child.
She would tell me these stories, and later, when she thought I was asleep, she would cry."
- In 'Frozen', the next mission in the story arc,we get to hear from the regular grunts of the Reman resistance... and it's not pretty. An example:
Player: Why are you fighting the Romulans?
Reman: My wife was working on a mining ship. This was not a military vessel. It had no weapons and limited shields. It was not in restricted space, and it threatened no one. The Tal Shiar captured it and "questioned" everyone on the crew for weeks. My wife died screaming in a Tal Shiar interrogation chamber. I fight for her.
Player: What do you want when this conflict ends?
Reman: What do I want? I cannot answer that question. All I wanted — all I will ever want — died with my wife.
- The Cardassian mission 'Badlands', when you learn the fate of the parents of Joshua Riker.
- In the mission "What Lies Beneath": When you find the latest victim of the crazy murderer, only seconds after she was begging for you to help her. AND once you realize the murderer was a hologram whose program degraded due to the radiation down there.
- In Delta Rising Gaul slaughtering the Talaxians, all in an attempt to anger you. Neelix doesn't rise to the bait and is just heartbroken.
- In the mission "Dust to Dust" the revived and turning-into-a-Kobali Harry Kim, frightened and confused, doing everything he can to get back to Voyager, not realizing what he's doing.
- The deaths of the Preservers in "Blood of Ancients". They spent millions of years in stasis in the hopes of one day meeting their descendents, only to be dispassionately wiped out by the Iconians.
- For the ground portion of Broken Circle, you will quickly round up a platoon of Red Shirts as backup, making the early parts of the mission quite easy. But as you travel between repeated engagements with M'tara expect your forces to dwindle until it's just your usual away team again. After that's done, the next map consists of flying through the ruins of your fleet which had been so huge at the start of the mission.. Your listed objectives are to scan for survivors, but the game cuts you off with instructions to just leave when you try.
- In the same mission there is a point where a Herald dreadnought is too powerful and Tom Paris gives the order to fall back. A Klingon captain says "I can't do that.. Today is a good day to die", as he revs up his engines and does a kamikaze to give everyone else a chance at hitting it.
- "Butterfly" has the team decide to use the Krenim weapon to stop the U.S.S. Yamato from discovering Iconia. It would stop the Iconian War altogether and bring back Romulus. Then, to your horror, you discover that, by doing so, the Borg have taken over Romulus.
- "Midnight" has you going back to the day the Iconians were eradicated. Just like Jean-Luc Picard postulated, they did nothing wrong. They might have been arrogant, but they were trying to protect other races and those races didn't like it.
- And Sela's reaction when she realizes the destruction of Romulus, and probably the entire Iconian war, are all her fault. It's the only moment in the game where she truly loses faith in herself, and for a second you think she might actually shoot herself out of despair.
- The entire mission of Renegades Regret which makes the player experience the Tzenkethi Coalitions genocidal actions through Neth Parrs point of view. This makes you feel for her and the civilians she was forced to kill. She then begs the admiral not to destroy a planet populated with billions only to be threatened by him before watching the planet get destroyed anyway.
- Some players may also feel guilty during parts of the mission since they must destroy ships with innocent civilians while they are pleading through the comms channel to spare them before detonating a protomatter bomb.
- The Mission "The Search" from the Gamma Quadrant series. Kira slapping Odo and calling him a Founder for intentionally luring the Hur'q to Bajor to get the Alliance in the war. It hurts because Odo destroyed a lifelong friendship in order to save people. The hurt on both sides is made apparent despite the limited graphics of the game's engine.
- The mission "Partisans"' ending. J'ula runs through rings to finally find proof that J'mpok was the mastermind behind the genocide at Khitomer... and watches in horror as the Great Houses decide that both sides suck and they should work alone. J'mpok decides to take up the vacant title of Emperor and J'ula realizes she destroyed her brother's work.
23rd Century Federation
- The last two TOS missions before the jump to the 25th Century is this:
- In "Painful Omens" you get to see what caused the Tholians to go after the Na'khul - time travelling Na'khul massacred a colony of Tholians and their Queen opted for a Taking You with Me to gain revenge, but not before telling the other Tholians that the Federation was not to blame.
- In "Battle of Caleb IV" you perform a Last Stand against a fleet of Klingon ships, giving your former Captain and the other ships a chance to escape. Even more, the captain, now Admiral, parts with a touching "Godspeed... and give them hell!"
- "Survivor" has the player, Agent Daniels and Sela arrive at an abandoned Tal Shiar prison and find evidence that Tasha Yar and the crew of the Enterprise-C is still alive when you hunt down the T'Nae from "Temporal Ambassador". You're given Hope Spot after Hope Spot that, somehow, Tasha is still alive only to learn that Tasha was one of the last to die, passing of old age and that her last request to T'Nae was for her to tell everyone the story of the Enterprise. At the end, Sela, once again in jail, is confronted by a Starfleet officer, who gives her a hologram of Tasha. Sela ends the mission by asking the person "Tell me about my mother...", the same thing Guinian asked Data of in "Yesterday's Enterprise".
- Compounding this is that confirmation that Tasha Yar isn't coming back.