Misaki Chronicles

 is an anime sequel to "Divergence Eve". It follows smoothly from the previous series. The characters are the same and the plot is similar, but the theme of the episodes is much different. In this series, the elite team at Watcher's Nest is traveling through time, fighting the Ghoul at different points in time during Earth's history, mostly in Japan. There's also some discussion about the fact that the different times to which they are traveling may also be different versions of Earth, on which the time-line is slightly altered. This series is also distinct from its predecessor in that it is more plot- and character-driven, with less in the way of fan service.
Episodes.
2327 - Lt. Commander Ertiana is keeping a journal, and explains that it's been sixty-years since they've set out into the Solar System. Due to her being the captain, it's necessary for her to stay awake, along with the crew, to make sure nothing goes wrong on the journey. She will spend approximately twenty-years of their mission awake while alternating shifts with two vice captains. A mission is patched in to the ship, which is from Misaki telling the potential receiver to inform Lt. Commander Ertiana that she is ok. The vessel comes in contact with Watcher's Nest, which indicates that there's still signs of a collapse. Lyar decides to explore the region and comes across Misaki's old room. She finds her journal there, which describes her experiences after first arriving at Watcher's Nest. After Lyar regains hope of making contact with Misaki, she can be seen running through Watcher's Nest as power is restored and the people are let out of their ships. There are a number of minor appearances from characters who had appeared in the previous series, and even this one, in periphery roles, including Luke Walker, the ice cream vendor from the Divergence Eve episodes "Specular" and "Designer's Children", and the girl who witnessed the specular of the Ghoul in "Specular". A woman can be made out prominently from the back, dressed in clothes similar to Luxandra in the opening theme song, looking at the schedule of flights. She is joined by a woman whose outfit greatly resembles Kiri's from the theme song and Misaki's memories. These two doppelgängers exchange glances, but only their faces above the nose are visible. The Luxandra-like woman's scars are noticeably absent from her face. Suzanna can also be seen working in a similar maintenance position as she was after her memories were altered in Divergence Eve. Professor Jalabert and Prim are also seen arriving, but not without the introduction of a woman whose face below the nose are not shown. Her appearance, including the color of the uniform, her eyes and the braid wrapped around her forehead, all resemble Lyar from her cadet days in the tenth episode, "Hidden Past". Guided by an apparition of Young Misaki, Lyar discovers Misaki materializing in her room, along with her journal. Misaki explains she's been waiting there for her the whole time. Lyar embraces Misaki in a warm hug, which closes out the series.
Characters.
Main Characters.
In episode 10, "Hidden Past", a model even older than Kotoko-01 appeared. She was presumably "Kotoko-00" and may have been the first model of android used on Watcher's Nest. Her appearance appeared to have traits of both the -01 and -02 model. She had a shade of pink hair closer to the -01 model, which was secured by clips that held them in Bunch-like pigtails while her outfit was sleeveless, more in line with the -02 model. She was under the command of a superior office during a time when Lyar was a new cadet. She had no dialogue in her short appearance, and unlike either of the upgraded versions, appeared colder and emotionless in comparison to the more inquisitive nature of -01 and exuberant nature of -02. 
In episode 11, "Hidden Past", while Kotoko is backing her memories up in the event of her destruction, LeBlanc is able to disable Kotoko after she discovers his plan to link the computer systems in Watcher's Nest to the mainframe in the ruins. Despite this, Prim is able to take control of Kotoko's body in order to help her stop Le Blanc. 
In episode 13, "Misaki", Lyar returns to greet Kotoko-02 after her repairs have been complete by Nodera. When she inquires as to the nature of Misaki, Kotoko reveals there is nothing in her memory banks about an individual with that name. She then inquires if Lyar is ok.
In episode 11, Prim attempts to takeover Kotoko's body after LeBlanc disables Kotoko. She gains control of it by the twelfth episode and manages to deliver her body to the "Integral System". Before LeBlanc can fire a fatal shot from his Rampant Armor, Prim manages to restrict the computer systems in his rampant armor, long enough for Misaki to fire the finishing shot. Misaki cannot initially bring herself to take the shot. Prim reveals why she had followed LeBlanc. The two are brother and sister, having been created from the same set of genes. LeBlanc's resistance causes greater damage to Prim's physical body, with LeBlanc eventually gaining the upper hand and telling Misaki that if she fires, she'll be killing Prim. She manages to hold LeBlanc at bay long enough for Misaki to fire, shattering the rampant armor and killing Prim.
In episode 13, "Misaki" when Lyar returns to Earth to inform her "family" of her demise, she encounters Jalabert. She begins to explain that Prim died in an accident involving an accelerator, but he informs her that Prim was never dispatched to Watcher's Nest. Prim would later be assigned to the project that intended to carry the displaced refugees back into the solar system in search of a planet, after Earth rejected their attempts to return to the planet. She and Suzanna would be seen working together, and Prim's background in theoretical physics allowed her to give further insight to parallel universes and how someone trapped in one could get back.