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  • The opening of the game contains this. You save the USS Khitomer, and you get back to your old ship... to find out that the entire senior staff you'd been talking to earlier are all dead now and that you and the ensign you met earlier on the Khitomer are now the senior staff on board. And it's time to go fight the Borg. And you do.
    • Specifically, the game opens with your character's first Crowning Moment of Awesome. In the middle of a massive starfleet battle, your character is sent over to assist the U.S.S. Khitomer. Going on a killing spree against the malfunctioning Borg on-board, you proceed to rescue the ship. It Got Worse is triumphantly prevented as your ship's command staff is executed by the Borg but you assume command and then take your vessel around to rescue the other damaged vessel's personnel. From there, you head down planetside to rescue a bunch of colonists from assimilation and then bring your ship around to join the fleet in blowing up a damaged Borg cube.
      • In a nice reversal of the Star Trek movie, while you're in command of your own starship at the end of the battle, you're still only promoted to a lieutenant's rank. Your vessel is also one of the smallest and weakest in Starfleet. Still, you can understand why Starfleet stands up and takes notice of your actions.
  • You escort a Vulcan ambassador to the monastery at P'jem. Once you arrive, the Klingons claim that the "ambassador" is in fact an Undine (aka Species 8472), and try to blow you up to get at him. Turns out... they're right. You fight the "ambassador", first on the ground, then you fight the Tethys-class dreadnought he has hidden in orbit, your officers noting with some panic that your little light cruiser doesn't have a prayer of beating it alone. You shoot down the plasma torpedos the dreadnought fires at you, trying to hold on... and then an entire fleet warps in and blows away the dreadnought. This is the second storyline mission after the tutorial.
  • You're sent to meet a contact who knows something about what a rogue Klingon "Ambassador" is plotting. She isn't in the Ferengi-owned bar you were supposed to meet her in, and the owner is playing dumb. How do you get him to talk? You play Odo to his Quark, and inspect his establishment for safety code violations, starting a bar brawl in the process.
  • You get to save the Enterprise from B'vat. Yes, that Enterprise, and you're in the past to start with because B'vat has kidnapped that Miral Paris. Later on in the mission, the Enterprise shows up to pay back the favor.
  • B'vat's last project before being defeated was resurrecting the Doomsday Machine to use against the Federation. His men succeed in his stead. You proceed to use nuclear torpedos powered by material from the core of a destroyed planet to destroy - yes, destroy - the Doomsday Machine by firing straight down its gullet, practically like Kirk did, all while a massive Federation fleet engages an equally massive Klingon fleet to ensure the Klingons don't stop you.
    • Also in the same mission, K'Valk steals a shuttle to do a Taking You with Me Heroic Sacrifice on the Doomsday Machine. While loudly singing the Klingon War Song. He fails but he does enough damage for you to be able to take it out.
  • "The Sisko has asked that we entrust this task to you." No spoilers, but that entire sequence, full stop.
    • Hell, most of the things that happen in Cardie space are awesome to varying degrees. The climax of it all is worth the price of admission to STO by itself, however.
  • So you're sent on what seems like a routine mission to meet another ship. You find it under attack by a Borg sphere and ride to the rescue... and then, out of nowhere, Q shows up, rewinds time, and makes you fight the Sphere again. You again defeat the Sphere... and Q rewinds time again, only now replacing the Sphere with a wing of Probes and demanding you do it one more time... with feeling! And then the three Borg cubes show up. "Intense, isn't it?" And that's just the intro to the real mission.
    • New Objective: Tell Q to Get On With It.
  • The Reman Feature Episode "Cutting The Cord" in its entirety. Your ship blasts through the Tal Shiar's planetary defenses, and you beam to the surface along with tons of Starfleet ground troops to raise some hell. Unfortunately, thanks to some local Applied Phlebotinum, your BOFFs have landed too far away to assist you. Is this a problem for you? Hell, no. You then proceed to wage an almost One-Man Army fight against the Tal Shiar, while calling in additional Starfleet reinforcements and orbital bombardment from your ship. This sequence culminates in you calling in an orbital strike to destroy a massive Iconian gateway...which your ship does with a full spread of Photon Torpedoes . And the mission isn't even over yet!
  • "Colosseum", the mission just before "Cutting the Cord", puts you in an arena and forces you to fight with melee weapons, including a Vulcan lirpa - while the famous music from "Amok Time" plays.
  • "Boldly they Rode", pretty much all of it. From EVA walking across the Dominion Captured Deep Space Nine station, to the final battle and the ENTERPRISE-F'S Big Damn Heroes entrance!
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