Please note that if you have not finished the original manga, then massive spoilers follow.
During the final battle between Athena's saints and the true body of Hades in Elysium (or Elysion, if you prefer), Hades looked into the eyes of the Pegasus saint Seiya, and remembered how ages ago, in the previous holy war, he was close friends with the previous Pegasus saint. We then cut back to the beginning of this holy war, in which two gold saints are sent by the pope to kill the boy destined to serve as Hades' vessel before the god of the underworld can take over his body. However, they are stopped by a young man named Tenma, who is a gifted cosmo user.
Later on, we cut to the present day, which in-universe means of 1990. After the final fight with Hades Seiya took a direct attack from Hades's cursed sword in order to defend Athena and give her the chance to destroy the dark god once and for all. As a result, Seiya fell into a catatonic state. Shun, hoping for answers, approaches Saori, who's taken it upon herself to watch over Seiya. She reveals that Hades' sword is still inside of Seiya, and that in three days, it will reach his heart and kill him. In order to save Seiya, Athena and Shun travel to the time of the previous holy war in order to destroy Hades' sword then, so that it may never be used on Seiya in the future.
- Action Girl:
- Saori/Athena fights in person for a few issues, then she's de-aged into a baby. Then she's back at that in Chapter 61.
- Shaina's still got it.
- Marin too.
- Art Evolution: The women in the book have curves and look quite feminine unlike the classic series.
- Badass in Distress: Seiya is Cursed by Hades and Callisto even sends Touma to murder him.
- De-Power: In two ways. The Bronze Boys lose their God Cloths and are downgraded back to their third version. Saori on the other hand gets reduced to a baby. For a while, at least.
- Dysfunctional Family: The Olympians, just as they were in Greek Mythology. Apparently Athena gets a lot of flak for fighting against her family members, despite this being a result of her simply trying to stop many of them from wiping out humanity.
- '80s Hair:
- Subverted with the Golds. The characters have shorter and more practical hair. Compare the beauty of Pisces Aphrodite with Pisces Cardinale.
- Played straight with Callisto.
- Future Me Scares Me: When Dohko sees what his future midget self will look like.
- Generation Xerox: Tenma is Seiya—to the point that Shun sometimes mixes them up. Also, some returning fans are complaining about how Kurumada is reusing many plot points from the original series. See History Repeats bellow.
- Healing Potion: Water when placed inside the cup that forms the Krater Cloth in its totem form.
- History Repeats: A Pope tries to kill Athena; a Gold Saint witnesses said act and flees with the baby, mortally wounded; Pisces Saint is an asshole; Taurus Saint dies standing, while protecting his temple; Gemini's temple is a maze (subverted in that the real Gemini Saint is actually present in his temple).
- I Did What I Had to Do:
- The Gold Saints sent to kill Alone before he can become Hades vessel aren't too enthusiastic about the task, and hope that Alone will be able to forgive them. In comes Tenma.
- Suikyo's reason for becoming a Specter is that Hades' followers are holding his little brother's soul hostage.
- Important Haircut: Saori when she uses it to trade with Hecate for directions.
- Impossible Task: The entire mission, according to Chronos, is a fool's errand because fate cannot be changed.
- MacGuffin: Hades' Sword is the cause of the plot, so they have to break it in the 18th Century.
- Meanwhile, in the Future
: The story keeps going back and forth between past and present as if everything was happening at the same time. The most jarring exemple being Shun in the 18th century having the feeling that something bad is about to happen to Seiya in the 20th century/ next page.
- Might be handwaveable by the fact they explicitly created a tie between the past and the present day that will hold only for three days.
- This would explain why the resurrection of the Ophiucus Gold Saint in the past affects Shaina in the present, and also why Aiolos' testament disappears from the wall in the future to reappear in the past to drive a point home to his predecessor.
- Moon Rabbit: Artemis' Satellites.
- Non-Action Guy: Seiya has been demoted to this, as he's pretty much comatose and dying.
- One-Winged Angel: Touma's scar on his back as well as his armor design.
- Present-Day Past: In order to avoid Comic-Book Time and Fridge Logic, the "present day" portions of the story take place in 1990, around when the original manga ended.
- Race Against the Clock: This is Saint Seiya after all, it just needs one like for every one of its arcs. Here, the heroes and Athena have 3 days (probably cosmic days at Chronos' scale otherwise we'd deal with Fridge Logic) to go to the past and break Hades' sword to save Seiya from a certain death due to the curse inflicted by said sword in his chest.
- One more layer when Athena gets struck by a poisonous snake and Odysseus himself is the only one who can cure her.
- Rank Up:
- Kurumada accepted the concept of Athena Saints being able to be promoted to higher Cloth Rankings, Shion and Dohko apparently were Bronze Saints prior to the story itself; oddly enough this wasn't brought up in the original series, going by how many times Seiya, Hyoga and Shiryu (and Shun and Ikki next to the very end) wore Gold Cloths, one would think they would be promoted by now.
- The dregs of Shaka's soul outright state to Shijima that Shun is his successor as bearer of the Virgo Cloth.
- Implied to inverted, and was about to played straight again, that the Ophiuchus Cloth was a Gold Cloth. The Ophiuchus Gold Saint was even said to have already obtained divine powers, which is why the Gods banished him away. As the Ophiuchus Temple re-emerges in the past when said Ophiuchus Gold Saint, Oddyseus, was about to resurrect, meanwhile in the present, Shaina got Brainwashed and Crazy and perhaps is possessed by Oddyseus.
- After a test of character, Kaiser acknowledges Ikki as the successor to the Leo Cloth.
- Likewise with Mystria who acknowledges Hyoga as his successor.
- Reptiles Are Abhorrent: Here, as the Ophiuchus Gold Saint returns, his Animal Motifs, the snakes, are out to tell people, chose to side with him or die. Ironically, in-universe snakes are thought to be the noblest animal in the Sanctuary due to their medicinal symbols.
- Set Right What Once Went Wrong: The whole reason they are going back is to destroy Hades' Sword that is in Seiya.
- Sliding Scale of Free Will vs. Fate: Saori believes she can save Seiya, Chronos tells her the fate "of the man in the wheelchair" can't be changed.
- Time-Delayed Death: Virgo Shijima has a white rose in his heart.
- Visions of Another Self: Seiya and Tenma, the only real example of perfect look-a-like between the two periods... Chekov's Gun for the impossible mission anyone?
- The Voice: Chronos/Khronos
- You Already Changed the Past: Before Saori/Athena was sent to the 18th century, there was no Athena present at this period; yet, in the 20th century's main story in the original manga, we learnt that during the previous war in the 18th century Athena was there with all her Saints. Therefore, Saori had already been taken into account as the Athena of the 18th century when the events are told to us in the 20th century even before we actually see her time travel. Thankfully, this has all been resolved as of chapter 62, when Kid!Saori tells Cardinale and Shijima that she is not their Athena, and that the Athena of the 18th century should be arriving at Sanctuary shortly.
- You Can't Fight Fate: Chronos tells Athena before she travels back in time that "the fate of the man in the wheel chair cannot be changed."
- You Shall Not Pass!: The 18th century Gold Saints to the Specters.