Anime/manga where the "forces of good" are the real evil

[Seiryuu]

I was wondering what some good shows were where the underlying forces that the hero serves turn out to be the ones they should be fighting. I'm thinking something like Tales of Symphonia, not like Scrapped Princess.

Spoiler for the difference:

In Scrapped Princess, the heroes start out fighting AGAINST the primary religion of the world, because if it is just and true like it claims then their little sister must die. From the first episode, it's clear which side is really evil and the good guys have determined to defy them.
In Tales of Symphonia, the quest begins with a mission of "salvation" intended to transform a girl into an angel in service to the Goddess who rules the world. For half the story, they think that the Goddess and Angels of Cruxis are holy, benevolent beings who wish to bring peace and prosperity to the world; eventually, they are forced to recognize that they've been working and struggling to realize a devised prophecy thought up by an enemy who's been manipulating them through the guise of divine messengers.

I'm not looking for something where the good guys are faced against a group that everyone else thinks is good, I'm looking for something where the good guys are actually working FOR this organization and completely believes that their superiors are acting wisely and justly to the benefit of all, not realizing their true face until they've contributed a great deal to the true enemy's plans.

Anime or manga will do, any rating so long as it has plot and isn't BL. No manhwa please, I can never remember the characters' names, so it's hard to follow.

[Daniel E.]

Originally Posted by Seiryuu

I'm not looking for something where the good guys are faced against a group that everyone else thinks is good, I'm looking for something where the good guys are actually working FOR this organization and completely believes that their superiors are acting wisely and justly to the benefit of all, not realizing their true face until they've contributed a great deal to the true enemy's plans.

Can only think of one title.....

Spoiler:

First thing in my head after reading this was Valkyrie Profile. There's a manga and a game and the second one fits your request like a glove.

I have never checked the manga, but if it's anything like the game then you can be certain that it will fill your request. I honestly recommend the game as well, btw.

[Kotohono]

Most definitely Darker than Black

Spoiler for Spoilers on plot for it:

The syndicate that most of the contractors work for, actual ultimate goal is to wipe all the contractors by any means necessary including using them to the full degree possible and at the cost of thousands of humans lives. And the syndicate not only played the contractors, but all the nations of the world.

And Fate/Stay Night perhaps

Spoiler for Spoilers on plot for it:

The "Holy Grail" that they were fighting for; is revealed to be an object of great evil that they never should have desired to obtain.

Mai-HiME, Fullmetal Alchemist, and Witch Hunter Robin should fit similarly to one of the two described above.

[Kafriel]

666 Satan, Air Gear, Berserk, Bleach (xD), One Piece. I'd say the feeling is most prominent in Air Gear and 666 Satan, but the other two have had their moments as well.

May I ask what's the point of giving such a request when you'll already be suspicious of something from the very first chapter? Kinda kills the twist...

[signorRossi]

f you tell you the name of a series now that fits your requirements don't I reveal instantly who is good and who is evil? :P

[OverMaster]

Excel Saga. But just because Excel is far too stupid to realize Il Palazzo is EVIL.

[Haak]

Definitely Fate/Stay Night but I would recommend playing the game rather than watching the two adaptions...

[CeDeR]

Demon Lord Dante fits perfectly...

[thevil1]

Noir (ノワール) - 26 episodes - Plot Summary: Mireille Bouquet is a professional assassin, and a very good one at that. But when she follows up an e-mail from a young Japanese girl named Yumura Kirika, inviting her to take "a pilgrimage to the past", her life becomes even more dangerous than it already is. Now, with a haunting melody invoking the memory of an event long past, Mireille and Kirika decide to work together to find the truth about a thousand year old organization that has controlled both of their lives since before they were born. And the only clue in their search, the only thing Kirika remembers about herself, becomes their working codename: a name designating an ancient fate, of two maidens who reign over death--Noir.

My thoughts on it: Noir was one of the first animes I fully watched, so to me, it's one of the best. For the request that you want, Noir fits your description perfectly.
Out of all the animes' I've watched, I would give Noir a 9.5/10 right behind Madlax.

Madlax (マドラックス) - 26 episodes - Plot Summary: In the country of Gazth-Sonika, civil war rages. There, a mercenary called Madlax plies her trade, with almost supernatural skill. In the seemingly peaceful country of Nafrece, Margaret Burton lives a tranquil life. As separate as their lives may seem, the two are connected by ties of mystery, and by a holy book that is also sought by the shadowy organisation, Anfan. As Margaret and Madlax follow the path of their destiny, they come ever closer to uncovering the truth - with no guarantee that it is a truth they can bear to learn.

My thoughts on it: I absolutely loved Madlax. It has a very complicated plot, and I still don't understand it fully. I watched it multiple times, and every time, I saw something new in it. due to the complexity of the plot, it's hard to say how accurately it falls under the category of your request. After watching the anime, it makes you re-think your definition of good and evil.
My overall rating of Madlax would be a 10/10.

Hope these suggestions are found useful.

[Dojima]

E's otherwise

It was a great anime, as how does it feel to be going against the people that gave you a home, to fight to save the people that can't stand you and fear you.

Wikipedia plot summery "Kai and Hikaru are protected by a corporation called ASHURUM, from a society that fears E's. ASHURUM is 1 of the 12 corporations that rule the world. Found by Eiji, Kai was selected to be in ASHURUM’s special force AESES and had to undergo intensive training in different areas, such as combat, hacking, and psychic training.

When Kai had free time he visited Hikaru at the hospital. Hikaru's condition never improved, however. After a year, Shen-lon warned Kai that Eiji actually only wanted his sister, because she was said to possess amazing psychic powers, but she was not able to use them due to her illness. Shen-lon then went on to tell Kai that Eiji was just hoping that Kai would have those amazing powers too.

Kai didn’t believe Shen-lon and goes on a mission to Gald city, with the other E's, to infiltrate a hideout of guerillas that is said to have been using E’s against their will. Kai finds some civilians caught in the middle of the battle. While trying to save a little girl, one of the civilians that is afraid of E’s, shoots and kills Kai’s partner.

Kai, still shocked from the death of his partner, tries to help the civilians, but meets up with Shen-lon. In a rage, Shen-lon unleashes a psychic blast that decimates half the city.

Later, Kai, washed up ashore, was found by a girl named Asuka. After being brought back to health, Kai was told by Yuuki, Asuka's brother, that he would not have his psychic powers back to the level they were unless he goes back to ASHURUM. However, after spending some time in the city with its residents, Kai decides to stay with Asuka and Yuuki for a while."

[pleasesavemyearth]

Anime:

Code Geass fits exactly what you're looking for. The main character is an exiled prince who, as the masked man Zero, starts a rebellion called the "Black Knights" in order to make a better world for his sister. Funny, with slight, almost unnoticeable ecchi.

Rainbow: Nisha Rokubō no Shichinin, is about a WWII disciplinary school, where a group of boys face the corrupted overseers, attempting to bring the school's dirty past to public light. A little Mature (No yaoi, promise.) at times, but lightens gradually as the series continues.

Daughter of Twenty Faces, about a young girl who is fascinated with detective novels and the mysterious thief, Twenty Faces. She's aware her aunt and uncle have been trying to poison her food, but still lives on miserably, until Twenty Faces himself takes her away to join his gang of thieves. PG-13 / 14+ rating, but mostly for violence.

Manga:

Mother Keeper takes place in a post-apocalyptic world where there are two societies, EDEN, a paradise that sucks the life out of the surrounding area, and the Outsiders, who live in poverty and usually live in rebel groups. The main character is Ricalna Forde, a brilliant sharpshooter for a rebel army. He dies on a mission to destroy the EDEN power source, only to be brought back as a robot EDEN "Mother Keeper."

And... that's all I can think of at the moment. = ^ _ ^ =

[SuzushinaYuriko]

Although it's a slight spoiler, Kiddy Grade. Its second half has a very serious and plot driven approach compared to the lighthearted first half. Also Macross Frontier to a degree.

[Kelis]

I think Kamikaze Kaitou Jeanne fits this request.

[Kafriel]

KIBA shows a very good example of this...

Spoiler for plot points, obviously spoilers:

especially Neotopia and later on with Tusk, but also in the beginning with Dumas.

[Seiryuu]

Thanks, there's lots of great suggestions. A few of these I've partly or fully read/watched, but had forgotten. For instance

Spoiler for since it is revealed late in the story:

Kamikaze Kaitou Jeanne really fits the bill. A girl has inherited the spirit or Joan of Arc, and is the only one who can stop the plots of the demons that have come to earth. However, the angel who is working with her is actually a fallen angel who is using her to collect the powers those demons have gathered and bring them back to be used to invade. And this angel plays her role well (and partly in earnest it turns out), so that the girl's fooled even after the invasion begins, and continues to believe in her friend until she sees fit to disillusion her and thus throw her into despair.

This is just what I'm talking about, a person fighting desperately in support of a "just cause" only to find out that they'd been duped into helping the enemy instead.

[~Yami~]

no other idea!

Code Geass is the best for you ^^