Amakusa 1637

Amakusa 1637 is a 12-volume manga by Michiyo Akaishi. It follows the adventures of six Japanese teenagers: Natsuki Hayami, Masaki Miyamoto, Naozumi Yatsuka, Eri Kasugano, Seika Akishima and Eiji Horie. They're classmates from a Catholic school in Kobe, and they barely survive the Great Hanshin Earthquake of 1995; five years later, during a school trip to Nagasaki, they get mysteriously transported... to the Amakusa region in the year 1637, shortly before the historical massacre of the Christian population.

Having been transported to different times, the six kids first must reunite with each other and assess their current situation, as well as what has changed between them since some arrived to a time set prior to the others's arrivals. And when they're done with it and gather their common knowledge of the future, they set out to exorcise their own inner demons as well as to prevent the carnage...

Tropes used in Amakusa 1637 include:

Action Girl: Natsuki is a Kendo expert and the sister of a Heir to the Dojo. Said abilities come off VERY handy when she's mistaken by a local swordsman.
Ambiguously Bi: Naozumi. He has felings for Natsuki ( which she rejects when he gives her an Anguished Declaration of Love), but is also said to yearn for Shirou.. Considering that he pretty much raped a prisioner Shirou and the Values Dissonance, he could toe into Depraved Bisexual or a practitioner of Situational Sexuality for some.
Asian Gal with White Guy: A Dutch captain named Jahn is interested in Seika/"Marina".
Battle Couple: Natsuki and Miyamoto, sorta.
Chronic Hero Syndrome: Natsuki, full stop.
- It also rubs on Miyamoto.
Downer Beginning: The manga starts in 1995, with the junior-high-aged Natsuki and Masaki barely surviving the Great Hanshin Earthquake that decimated their city, Kobe. In-story, said 'quake actually was caused by the same phenomenon that would throw the kids in the past six years later.
The Dulcinea Effect: Jahn saved Seika's life when she arrived to the past and fell for her. She doesn't necessarily reciprocate, though.
Dude Looks Like a Lady: Shirou Masuda aka Shiro Amakusa. (Somewhat Truth in Television, as he was described as a very handsome young Samurai).
- Identical Stranger: Natsuki looks a LOT like Shirou (only younger and female), and this is a BIG plot point since the people believe her to be either Shirou or an angel that took Shirou's form to help them.
Gadgeteer Genius: Eiji
Girlish Pigtails: Eri braids her hair
Heel Face Turn: Occur frequently among those exposed to Natsuki.
Historical Domain Character: Shiro Amakusa, Tokugawa Iemitsu, Yagyu Jubei, the Nabeshima clan, etc. Even more so: Masaki became none other than Miyamoto Musashi.
Love Dodecahedron: Natsuki loves Miyamoto. Miyamoto loves her but later is amnesiac -- but he falls again for her when he recovers his memories. Naozumi loves Natsuki and also Shirou, though he also saw him as a Replacement Goldfish. Otsu loves Miyamoto...
Japanese Christian: Both the peasants and the students.
Maybe Magic, Maybe Mundane: The locals believe the time-travelers to be messengers from "Deus". The time-travelers are a lot less certain, and know that their "miracles" have mundane explanations, but some of the coincidences are troubling
Meaningful Rename: Seika is also known as "Mariana", her Christian name. Natsuki is first referred to as "Francisco-sama" and later as Shirou. Naozumi is renamed as Kotada... and Masaki, as Miyamoto Musashi.
The Messiah : Natsuki's greatest strength is her ability to unite others behind her through sheer kindness. The real Shirou also was this... but he was much less fortunate.
Mission from God : Seika is confident the group is on one. Her confidence isn't necessarily shared.
Mundane Afterlife: Inverted. At one point, the locals ask the protagonists to describe the "Heaven" they believe they come from. When the protagonists comply, they are themselves shocked and moved when they realize the modern society they describe - one of electric light and heating, religious tolerance, rule of law, and ample food - is, in fact, Heaven for the medieval peasants. A paradise that they'd been taking for granted.
Romantic Two-Girl Friendship: Eri and Natsuki.
Saintly Church : The protagonists seem to be forming a proto-example of this.
Set Right What Once Went Wrong : The protagonists' goal throughout the series. They succeed, resulting in a modified, apparently better timeline.
The Strategist: Eri is the brains to Natsuki's Action Girl-like brawns.
Student Council President: Natsuki, with Masashi as her vice-president. That is, before they get thrown back in time.
Time Travel
Trapped in the Past : In the end, all but one protagonist remain in the 17th century. Only Eri returns to our era, finding it changed for the better by the group's actions.
Cell Phones Always Existed : Justified; the cell phones only work when the phenomena that caused the time travel is active (allowing communication to pass through modern-day satellite infrastructure).
Write Back to the Future : Well, more like leave sealed cell phones to be found in the future.