Star Trek: Millennium

A trilogy of novels in the Star Trek Expanded Universe, an epic time-travel adventure featuring the characters of Star Trek: Deep Space Nine. It doesn't fit entirely into the modern continuity, but given the themes of myriad alternate realities and interlinking timelines, that isn't a problem either way. The three books are The Fall of Terok Nor, The War of the Prophets and Inferno, and the plot involves a full-scale religious war erupting in an alternate future timeline, the result of an attempt by factions of the Wormhole Aliens to reunite their splintered civilization. Unfortunately, success will mean the end of the universe.

The trilogy shares a great many plot points with the Deep Space Nine computer game, The Fallen.

"Can I have an Amojan?!!"
 * Action Girl: She's a bit older than most, but Vash probably counts. Her Andorian rivals, Satr and Leen, are Dark Action Girls.
 * Affably Evil: Weyoun, most of the time.
 * After the End: Book Three, Inferno, takes place . It's complicated...
 * Alien Arts Are Appreciated
 * Alternative Calendar: A reasonably important plot point concerns a possibly non-coincidental similarity between multiple cultures' otherwise distinct calendars.
 * Anyone Can Die: Once we're in the alternate future, any character encountered (no matter how familiar or otherwise protected by Contractual Immortality) can die. In fact, most do.
 * Badass Preacher: Obanak Keelen.
 * Big Bad: At first it looks to be Weyoun. Then...things get complicated.
 * Bizarre Alien Biology: The Grigari appear to be a mechanical-organic construct. No-one is sure whether they should be categorized as living beings or an artificial intelligence. They leak a substance that might be blood, or might be cooling fluid.
 * Blatant Lies: When Dr. Bashir asks Garak to aid him in identifying two recently-discovered bodies, Garak responds: “Oh, Doctor, I'm afraid that in matters of mysterious deaths, I am entirely bereft of experience”. No-one is amused.
 * Blessed with Suck: Anyone corrupted by Grigari nanites; they give the host superior strength, regenerative abilities and other powers, but also reconfigure their brain, making them compliant servants of the pah-wraiths.
 * Body Horror: Bions - the lobotomized, bio-augmented slave soldiers used by the future Romulan Empire. It's suspected they are former prisoners mutated using Grigari technology.
 * Brain Food: The Medusans, apparently. Quark has certain recipies programmed into the food replicators (quite illegally), should he ever get a visit from a Medusan delegation.
 * Brainwashed: Weyoun, having been freed from his genetically mandated loyalty to the Founders, doesn't realize he has simply been transferred to a new master in the Grigari.
 * The Chessmaster: Obanak Keelen is possibly the finest example in the Star Trek universe. He sets into motion a plan that involves muliple timelines, several realities, and the end of the universe, manipulating not only the heroes and villains both but also his own gods.
 * Church Militant: Pretty much everyone in the alternate future. They even have a warship named the Opaka (which really alerts the time-displaced heroes that something is wrong, because Opaka was a woman of peace and preached a non-aggressive, tolerant faith).
 * Cool Ship: In the alternate future, the Timeship Phoenix. Also from that future, the Enterprise-F, though it ended up being obliterated in the first eight minutes of the battle to save Earth from the Grigari.
 * The Corruption: Grigari nanites.
 * Cosmic Keystone: The Red Orbs of Jalbador. When all three are brought together in one place, they open.
 * Crapsack World: In the alternate future, Earth has been destroyed by the Grigari, its colonies wiped out by nanoplagues, humans, Klingons and Cardassians are all nearly extinct, what's left of the crumbling Federation is at war with the Bajoran Ascendancy, which worships the Pah-wraiths and is led by, and his ultimate goal is to destroy the universe.
 * Cultural Posturing: A Bajoran mentions how her people were architects and artists when "Cardassians were still swimming through swamps catching fish in their mouths".
 * Dangerously Genre Savvy: Weyoun. Garak, too, though he doesn't act on the observations he makes, having decided that since Cardassia no longer exists in this future, he has nothing more to fight for. He basically sits this one out, and spends most of his time calmly and somewhat cheerfully making Genre Savvy comments to annoy Odo.
 * Dyson Sphere: In the alternate future, O'Brien is trapped in one of these for what seems like years, as the Fate Worse Than Death meted to him by the Pah-Wraiths.
 * Earth Is the Center of the Universe: Not so in this case. This being Star Trek: Deep Space Nine, Bajor seems to be the center of the universe instead.
 * Earthshattering Kaboom:.
 * Enemy Mine: The Grigari are so terrifying that the Borg and the remnant Federation are allies in this timeline. It doesn't even seem to be Teeth-Clenched Teamwork; they're engaged in peaceful technological exchange.
 * Fate Worse Than Death: Dukat and Kosst Amojan trap the heroes in recurring personal nightmares in order to gain their co-operation. Basically, they trap them in personal hells, sometimes along the lines of And I Must Scream. Unfortunately for Dukat, it doesn't work on Dax; her multiple lives confuse the Kosst Amojan, which tries creating multiple hells that then just blend together confusingly and lose their horror, allowing her to break free. And Garak isn't impressed by the technique - his hell certainly works on him, but Dukat is frustrated to see that he isn't actually afraid - exhausted, drained, horrified, yes; but nowhere near afraid.
 * The Gods Must Be Lazy: The pah-wraiths are far more proactive than the Prophets. This is actually justified - the Prophets' best bet for protecting the universe is to keep their distance and remain apart from the mortal/temporal realm, while the pah-wraiths want to bridge the distance and reunite with their brethren, even though it means destroying creation.
 * Godzilla Threshold: Not only has the Federation made allies of the Borg, they're engaged in multiple attempts to alter the timeline despite several reasons to think this is a bad idea and have suspended the Prime Directive to allow an invasion of the Mirror Universe in hopes of creating a safe haven there.
 * The Greys: Implicitly, the Reticulii.
 * I Believe I Can Fly: Weyoun can levitate, thanks to the Wormhole Aliens.
 * Impossibly Cool Weapon: The electric mini-bat'leth wielded by Base.
 * It Got Worse: Deep Space Nine is destroyed and the heroes are flung decades into the future - that's the end of the first book. In the second book, they discover that this future is a Crapsack World where Starfleet is a Church Militant organization fighting an interstellar doomsday cult, led by . Then they discover this doomsday is actually real...and that the enemy is planning to destroy the universe.
 * Large Ham: We can't actually hear him, of course, but there's no way Kosst Dukat isn't this.
 * Loss of Identity: To Jean-Luc Picard, of all people. By 2400, his Irumodic Syndrome has progressed to the point where he has lost almost all contact with reality, forever having imaginary conversations with his long-dead friends from the Enterprise-D. And he's basically in charge of Starfleet.
 * Missing Time: Neither Odo, Quark or Garak can recall what happened the night of the Cardassian withdrawal from Terok Nor. Quark is the only one who will admit it, though. His attempt to find answers irritates Odo and Garak, who refuse to discuss or acknowledge that they're in the same situation.
 * My Species Doth Protest Too Much: Arla Rees. A Bajoran athiest, she is actively and somewhat obsessively opposed to her people's faith, believing the Prophets to be conquering aliens who have stunted Bajoran culture in order to keep them passive and compliant. She bitterly acknowledges how at odds she is with the rest of her people, saying that sometimes she thinks she's the only one who "sees it".
 * Nanomachines: The Grigari use these; they serve as The Corruption.
 * The Napoleon: Base, the world's smallest and most angrily homicidal Ferengi.
 * Not So Harmless: Future Weyoun is Affably Evil, and also a little comical. He is not to be underestimated, though, and when he tires of the heroes' interference, he shows just how dangerous he is. He also managed to.
 * Omnicidal Maniac: Dukat and Kosst Amojan. They aren't the only people out to destroy creation, but the others have far more sensical motives.
 * The Phoenix: The Romulans have a similar myth; in their culture, the flaming bird is Alth'Indor.
 * Prophecy Twist: The Bajoran religious prophecies, along with the basic principles of the faith itself, were written.
 * Retroactive Precognition: Many of the more notable Bajoran prophecies, thanks to the Timeship Phoenix.
 * Rousing Speech: Amusingly, Weyoun doesn't feel the need to give one as the day of the final reckoning dawns.
 * Scary Dogmatic Aliens: The Grigari, who are fanatical and deadly enough to scare the Borg. The Bajoran Ascendancy, which is one giant doomsday cult fighting to destroy the universe. The Wormhole Aliens, which are fighting a three-way war that threatens to tear the mortal realm apart. Even the newly Vulcan-dominated Starfleet. And we mustn't forget Kosst Dukat:


 * Sealed Evil in a Can: Kosst Amojan and his followers (the banished pah-wraiths cast from the Celestial Temple into the Fire Caves). However, the straightforward pah-wraith plotline of the TV series, which disappointed some fans in its bog-standard simplicity, is made far more complex here. For one thing, the Fire Cave pah-wraiths are not the only ones; indeed, they're a minority. They no more represent the pah-wraiths as a whole than they do the prophets.
 * Servant Race: The Grigari seem to be servants of the Ascendancy,.
 * Sibling Team: The Andorian sisters Satr and Leen, in the first book.
 * Stable Time Loop: The War of the Prophets is a stable time loop that transcends a single timeline, and connects multiple realities together. It's hinted in the epilogue that all timelines are linked, and ultimately part of a larger network, that might one day be explored just as the Federation explores space.
 * The Voiceless: Played with but ultimately reaffirmed for Morn. Just as Morn never speaks on screen, so the novels never give him dialogue (despite mentioning how he's actually a chatterbox). In the first book of this trilogy, it briefly looks like Morn has been giving dialogue as part of a Crowning Moment of Awesome. Turns out it's actually Odo taking Morn's form.
 * We Come in Peace, Shoot to Kill: This is used as a cover story by the Grigari in the alternate future. They "mistook Earth's intense sensor scans" for an attack, then "fired a warning shot" that they "didn't realize would overwhelm the planetary defenses". Result: Earthshattering Kaboom.
 * Weapon of Mass Destruction: Quite a few in the Crapsack World future, including a nova bomb, nanoplagues and planet-destroying "deep time" bombs.
 * Well-Intentioned Extremist: Sisko wonders if Leej Terrell is this. At first she seems nothing more than a megalomaniac and Complete Monster, but Sisko begins to consider if she's actually serious about her proposed "pax Cardassia". The golden age she says she's working for might be a genuine dream - not that it excuses her actions.
 * Wounded Gazelle Gambit: Vash appears to have been hit by a toxic dart in an assassination attempt, and is rushed to the infirmary, unconscious. The poison is an Andorian neurotoxin, implicating the Andorians Satr and Leen, who are rivals to Vash (and particularly shady characters). It is not in fact fatal to Humans, though, and Vash fully recovers. She later mentions the toxin by name in a throw-away comment, alerting Bashir that she planned the whole thing - because he never mentioned the name, and there are dozens of neurotoxins it could have been. It turns out Vash injected herself with the dart.
 * Xanatos Roulette: The most epic in all of Trek, pulled by Obanak Keelen. Everything that happens in the trilogy unfolded according to his plan. That plan involved blowing up the universe and then helping the universe get better. It also involved using the gods themselves as pawns (okay, the Wormhole Aliens are only gods to the Bajorans- but Obanak is a Bajoran).