The plot is a bit difficult to wrap your brain around. In 2017, Earth satellites detect a gravitational anomaly coming from the direction of the constellation Lyra. When the signal is analyzed, it's revealed to be a transmission from the Voyager spacecraft, leading to the discovery of faster-than-light travel as well as a wormhole inside the core of Saturn's moon Titan. Others are soon discovered. Further exploration of these wormholes, or "inflation holes," results in the discovery, in the year 2197, of a planet ten parsecs from Titan which is dubbed the Quantum Core, which contains a wormhole identical to Titan's at its center and was apparently once occupied by a now-extinct alien species whose excessive use of wormhole travel resulted in the equatorial mass of the Core being burned away, leaving it in the shape of...well, an apple core.
Within 50 years, humanity has constructed a base on the Core, dubbed Watcher's Nest. Not long after, an expedition beneath the planet's surface is attacked by a Ghoul - your garden-variety Eldritch Abomination, origins and intentions unknown. The purpose of Watcher's Nest is now twofold: Monitor the Core, and prevent any further incursion from the Ghoul. Autopsies and genetic research conducted by a group called Alchemy reveal startling results when Ghoul genes are combined with animal DNA — and later with human DNA, resulting in the project being officially closed down.
Now a new squad of cadets is brought on board Watcher's Nest to experience combat training, conspiracy and absurdly tight uniforms. Misaki, our heroine, is hardly cut out for the job — but trouble seems to find her, and she's being observed by parties unknown....
The original series was followed by a second 13-episode series, Divergence Eve: Misaki Chronicles, in 2004. With the same set of characters and set in an alternative universe, Misaki Chronicles is about the elite team at Watcher's Nest defeating Ghouls at different times in Earth's history.
This anime provides examples of:
- Anachronic Order: Confused by the first episode? You should be, as it takes place chronologically between episodes 12 and 13.
- Anime Hair: Compared to other anime the hair isn't too extreme, but most defy physics.
- Artistic License – Military: Luke Walker is identified as a chief petty officer in early dialogue but his bio in the opening credits lists his rank as sergeant. And no, the Japanese words for the ranks aren't the same.
- Big "NO!": In episode 10 Luxandra screams "no!" as she dies.
- Clothing Damage: Clothing, and especially space suits, seem to be made of wet tissue paper. Every time Misaki transforms, her armor rips off, leaving her naked. How else do you expect to see as much cleavage as you do in here?
- Eaten Alive: Luxandra is devoured by a ghoul in episode 11.
- Eldritch Abomination: The Ghoul is identified as a being from an Alternate Universe that is able to cross into "our" universe because the wormholes used for Faster-Than-Light Travel pass through alternate universes on their way in, which apparently weakens the boundary.
- Empty Shell: Misaki becomes this in the final episode after remembering "her" death.
- Expendable Clone: The clone of Misaki who dies in episode one.
- Fanservice: Dear God in heaven. Every single female character save Kotoko is quite buxom and bouncy, and Misaki in particular gets a lot of underwear scenes and invariably ends up completely losing her flight suit when she transforms.
- Gory Discretion Shot: When Luxandra is Eaten Alive nothing is seen except the blood.
- He Knows Too Much: LeBlanc says this before he kills Bernard: "The rat has entered the forbidden zone."
- Immortality Seeker: LeBlanc's ultimate goal is to get unlimited power through the knowledge of the universe.
- Intrepid Reporter: Subverted. Bernard Firestar turns out to be a complete ass and gets himself shot by LeBlanc.
- Laser-Guided Amnesia: This happens to anybody who leaves the military having learnt top secret information to stop it leaking. This happens to Suzanna.
- Mecha: Rampart Armor is a Military Mashup Machine of a roughly twice-human-sized mecha and a Space Fighter, designed to fight both on the ground as a brawler/machine gunner and in zero gravity, with a detachable cockpit that acts as an Escape Pod.
- Mind-Control Device: LeBlanc uses a microchip to control Misaki's body since her "heart is empty".
- Mood Whiplash: The end credits of the first series features imagery of Misaki frolicking in skimpy swimsuits set to a bouncy J-pop song, which invariably comes right after a dark sci-fi metaphysics moment.
- No Hugging, No Kissing: Except for the Fake-Out Make-Out there's no touching at all. No romance either.
- Not Using the "Z" Word: They are zombies. "Energy is sent to their brains while their bodies remain."
- People Jars: Hundreds of them kept by LeBlanc and, worst of all, they aren't dead.
- Soundtrack Dissonance: The ending theme of the first series and the opening theme of Misaki Chronicles are bouncy pop songs.
- Stripperiffic: Kotoko's pilot-suits in both seasons, the second even more so. Even her casual outfits tend to show a good amount of skin.
- These Are Things Man Was Not Meant to Know: In the final episode LeBlanc learns of all the knowledge in the entire universe and their head explodes.
- Tomato in the Mirror: It's obvious to the audience from the start that there's something special about Misaki. All in all she's the second generation of generically altered humans (altered by the Ghoul) with makes them special in various ways. She is also a connection to the Ghouls.
- It also turns out that Prim is one as well, but caused different results.
- World of Buxom: Every single female character apart from the flat-chested gynoid Kotoko is quite stacked and prone to bouncing. This is pure visual fanservice that plays zero part in the series' story.
- Vapor Wear: The training outfits the cadets wear. Also there's Kotoko's...unusual style of pilot suits.
Misaki Chronicles contains the following tropes:
- Beethoven Was an Alien Spy: Toyotomi Hideyoshi was a Ghoul.
- Brain Uploading: LeBlanc throughout the new universe is littered through the computer system and manages to control it. Eventually a host body is created.
- Brutal Honesty: After Lyar says a heartfelt farewell to Kurenai-no-ha when she returns to the sort of future, Kotoko finds out what would happen to him he gets executed for trying to kill Toyotomi. She jokes about what would have happened had Lyar gone and helped him.
- Convenient Coma: Prim is in a coma throughout the series but she manages to connect herself to the computers in time to fight against LeBlanc.
- Cute Ghost Girl: The child version of the original Misaki... who was created by the original Misaki.
- Dead Person Conversation: Misaki with her dead father prior to the last episode which gives her a change of heart.
- Distant Finale: Lyar is shown to be somewhere in her fifties and finds Misaki (the same age but no longer a ghost) again.
- Freudian Excuse: LeBlanc has mother issues.
- Ghost Memory: 1595-Misaki gets the memories of dead people. She experiences the death of the original Luxandra, because that was sort-of in the past.
- I Never Told You My Name: Lyar asks Kurenai-no-ha how he knew her name; he says that he heard Kotoko say it, which was a lie.
- Laser-Guided Amnesia: Suzanna's previously erased memories are restored.
- Military School: Part of Misaki Chronicles takes place during the characters' training in the alternative universe.
- Mind Screw: They're travelling to the past of an alternative world while also being trapped outside of time... It gets complicated.
- Past-Life Memories: The new Misaki remembers her previous self from the original anime.
- Ret-Gone: After sending Lyar, Kotoko, and Suzanna back to the correct universe after she gets trapped, Misaki effectively does this to herself. Lyar is the only one who remembers her.
- Samurai: Kurenai-no-ha.
- Set Right What Once Went Wrong: Misaki's goal is to save loads of people from dying in this new timeline, trying to find an alternative world "without sadness". She comes to the conclusion that this isn't possible.
- Trapped in the Past: There's a time limit for how long the barrier around Earth will remain open. If they stay too long whoever went down would become trapped. Though really the original Watcher's Nest has become trapped outside of time and has overlapped with another part.