From Viz:
Phoenix is made up 12 complex stories linked by the presence of the mythical bird, an immortal guardian of the universal life force. Read in order, the separate stories jump across time, alternating between a distant future and a distant past, converging on the present, with characters from one story being reincarnated in another. The 12 stories--over 3000 pages.

Dawn:
The first volume, originally serialized in 1967. This story takes place in 240-270 AD, in the era of Queen Himiko of the Yamataikoku. Using her army, led by feudal general Sarutahiko, to invade Japan, she seeks the Phoenix and eternal youth.

Future:
The second volume, originally serialized in 1967-68. In Phoenix's chronology, this is the final story; it takes place near the end of mankind. In 3404 AD, the world has become super-modernized, but humanity has reached its peak and shows decline. A young man named Masato Yamanobe is living with his girlfriend, Tamami, a shapeshifting alien. Pursued by Masato's boss, Rock, they eventually take shelter at the isolated base of mad scientist Dr. Saruta, who attempts to preserve life on Earth with the assistance of his robot, Robita. Eventually, nuclear war breaks out.

Yamato:
The third volume, originally serialized in 1968-69. This story takes place in 320-350 AD (Kofun period), and is based on the Yamato-takeru-no-mikoto legend. The decadent king of Yamato is trying to have his own version of Japan's history written. Meanwhile, a "barbarian" tribe, the Kumaso, is writing an unbiased history. The king of Yamato sends his youngest son, Oguna, to murder the barbarian chief, Takeru. On his journey, Oguna encounters the Phoenix.

Universe:
The fourth volume, originally serialized in 1969; also known as Space. The story takes place in 2577 AD, where four astronauts must escape their ruined spaceship in escape pods. The survivors eventually crash into a mysterious planet. Among them is Saruta, who contends with Makimura for the heart of their female companion, Nana. On this strange planet, they eventually meet the Phoenix.

Hō-ō:
The fifth volume, originally serialized in 1969-1970. The story occurs in 720-752 AD. (the period in which the Daibutsu of Todaiji was built), during the Nara period. One-eyed and one-armed young man Gao, an ancestor of Saruta, turns into a murderous bandit when he is rejected by his village. He attacks a sculptor, Akanemaru, and the two men's paths diverge, but their fates remain linked. Akanemaru becomes obsessed with the Phoenix to the point that he loses sight of his original dreams, while Gao eventually finds a state of grace despite his continuing hardships. Ho-ō is widely considered the masterpiece of the Phoenix series. This became the basis of a Famicom game, in which Gao is the playable character.

Resurrection:
The sixth volume, originally serialized in 1970-1971. The story takes place in 2482-3344 AD. In an age of robotics, technology and science, young Leon dies in a car accident. He is returned to life by scientific surgery, but his now mostly-artificial brain makes him see living things -- including humans -- as distorted clay figures, while he sees machines and robots as beauties. Leon falls in love with a worker robot, Chihiro, whom he sees as a beautiful girl, and will fight for this forbidden love. He will also find out the secret behind his accident. A side plot features the robot Robita, who previously appeared in Future.

Robe of Feathers:
Serialized in COM, 1971. Published in English by Viz as an appendix to the second volume of Civil War (Turbulent Times). Based on the story of the Hagoromo.

Nostalgia:
Published in COM, 1971; continued in Manga Shōnen, 1976-1978. A science fiction epic about the rise & fall of civilization on the deceptively named desert planet of Eden & one boy's universe-spanning search for the planet of his ancestors: Earth. Features numerous cameos from other Science-fiction based Phoenix stories, including the shape-shifting alien "Moopies" first seen in Future, Makimura from Universe & an early model Chihiro Robot from Resurrection.

Turbulent Times:
Published in Manga Shōnen, 1978-1980. The story is about a woodcutter named Benta and his childhood sweetheart, Obu, who are separated and caught up in the events of the Genpei War. Various historical figures, such as Taira no Kiyomori, appear as major and minor characters. The character of Gao (from Ho-ō) appears as a 400-year-old hermit.

The Viz (English) edition is entitled Civil War and is split into two volumes, with Robe of Feathers included as an appendix to the second volume.

Life:
Published in Manga Shōnen, 1980. A TV producer who attempts to procure human clones to use in a The Most Dangerous Game-style reality TV program learns the error of his ways when he is mistaken for a clone himself. This episode is notable for only featuring the Phoenix in flashbacks and also for introducing her half-human daughter who does not appear again after this episode.

Strange Beings:
Published in Manga Shōnen, 1981. The story of a female samurai who is imprisoned in a time-warp by the Phoenix as punishment for her sins along with her faithful retainer & forced to become a healer treating the victims of wars from all over time and space including humans, youkai and various extraterrestrials. This chapter was loosely based on the Hyakki Yakō emakimono by the famous Japanese artist Tosa Mitsunobu (although in the context of the story it's the complete reverse).

Sun:
Published in The Wild Age, 1986-1988. This is the longest story, and was the final volume completed before Tezuka's death. It centres around Harima, a young Korean soldier from the Baekje Kingdom whose head is replaced with that of a wolf by Tang Dynasty soldiers following the defeat of the joint Baekje-Yamato force at the Battle of Baekgang. He then escapes to Japan where he becomes the feudal lord Inukami and becomes caught in the middle of the Jinshin War, as well as joining a greater battle between supernatural forces and time-travelling to a bleak future world ruled by a theocracy that claim to have captured the Phoenix. This chapter stands in stark contrast to the earlier historical Phoenix stories, which tended to de-mythologize the mythical characters therein, for instance in Dawn, many Shinto gods are portrayed as mere humans. In this chapter, however, various Youkai, Oni, Tengu and other mythical creatures are shown fighting against Bodhisattva.

Early Works:
Covers the prototype version of the series from the 1950s.