Universal Century 0068, Side 3 - The Autonomous Republic of Munzo. Zeon Zum Deikun attempts to declare complete independence of Munzo from the Earth Federation Government, while he preaches the evolutionary potential of humans who have advanced into outer space. Deikun however suddenly falls to his death in the middle of his speech at parliament. Upon Deikun's death, Jimba Ral spreads word of a House of Zabi conspiracy - but despite such efforts the power and sphere of influence of House of Zabi, led by Degwin Sodo Zabi, only seem to escalate. While we witness for the first time the untold convulsions of Universal Century history, Casval and Artesia, just bereaved of their father, must face destinies which will be just as tumultuous as the very era itself.

While the perfect getaway for most girls her age might be a fancy vacation with their loved ones, Rin Shima's ideal way of spending her days off is camping alone at the base of Mount Fuji. From pitching her tent to gathering firewood, she has always done everything by herself, and has no plans of leaving her little solitary world.

However, what starts off as one of Rin's usual camping sessions somehow ends up as a surprise get-together for two when the lost Nadeshiko Kagamihara is forced to take refuge at her campsite. And even after Nadeshiko's sister finally picks her up later that night, both girls silently ponder the possibility of another camping trip together.

In an underground world where tunnels extend everywhere, even though they live in dark and confined spaces, people wear protective clothes and lead quiet and enjoyable lives. Patema, a princess in her underground village, loves to explore the tunnels. Her favorite place is a "danger zone" that her village prohibits people from entering. Even though she's scolded, Patema's curiosity can't be held back. No one ever explained what the supposed danger was. On her usual trip to the "danger zone," Patema faces unexpected events. When hidden secrets come to light, the story begins to unfold.

国立爱丽丝研究机关学园本部不同于一般的学园，只招收具备特殊能力的学生，这种能力被称之为“爱丽丝”。因为好友今井萤（钉宫理惠 配音）转学从乡间来到了城里的爱丽丝学园，无论如何也不想和萤分开的佐仓蜜柑（植村加奈 配音）因此离家出走，跟随萤来到了学园。但没有超能力的她根本无法进入，被学院老师鸣海先生（石田彰 配音）救助后，意外地开发了蜜柑的超能力，于是，机缘巧合下，蜜柑也进入了爱丽丝学园，达成了她和萤在一起的愿望。
新学校的生活有喜有忧。蜜柑所具备的超能力被同学嗤笑为最无用能力，和其搭档的又是问题少年日向枣（朴璐美 配音），不能见相依为命的爷爷，在各种挫折困难面前，蜜柑依然乐观应对，逐渐赢得了大家的喜欢，也收获了和枣的爱情，但前路依旧有各种困难在等着他们……

中世纪，炼金术士们以巨大的代价从恶魔的手中得到了传说中的永生之酒，凡是喝下永生之酒的人们，正如它的名字那样，将会得到永远不会死亡的肉体。永生之酒带来了希望，却也引发了空前绝后的灾难，因为私欲和利益，与此酒相关的人士一个接着一个失去了踪迹。随着禁酒令的颁布，永生之酒的下落逐渐成为了谜题，然而数年过后，有关它重出江湖的消息再次被传得沸沸扬扬，在纽约的黑道中激起了涟漪。
身怀绝技的少年洛菲（吉野裕行 配音）、不老不死的炼金术士阿洛瓦（宫本充 配音）、个性莽撞大大咧咧的夫妻艾萨克（小野坂昌也 配音）和哈文特（青木静香 配音），这些身份从无交集的人们，也为了追寻永生之酒的下落而走到了一起。