For many, Assassin's Creed 3 doesn't rank high on the long list of Assassin's Creed games for a variety of reasons, but there's little doubt that it was one of the high moments for the franchise in terms of the modern-day storyline. It introduced a major plot point involving the first civilization Juno that many expected to be extensively explored throughout the following games, and to some extent, it did. However, many noticed her lack of real presence in Assassin's Creed Origins and Assassin's Creed Odyssey.
In some ways, this is because Juno's storyline has been resolved, but unless players had been keeping up with the printed stories of Assassin's Creed, this is easily missed. Therefore, here's what happened to Juno in the Assassin's Creed franchise. NOTE: This article will contain MAJOR SPOILERS for several Assassin's Creed games and Assassin's Creed Uprising.
Assassin's Creed 3 ends with Desmond giving his life to save the world but consequently releasing Juno at the same time. He did this with faith in the Assassins that they could stop her dastardly plans. The following games did something to the modern-day storyline that many did not like: the modern-day Assassin became the player in an awkward first-person mode. Still, Juno's story moved forward into Assassin's Creed IV: Black Flag.
Black Flag showed Juno continuing to manipulate current-day events, as well as introducing the Sage, who is a heterochromatic individual born with the memories of Aita, Juno's husband. Sages are typically driven mad by these memories, but each is essentially devoted to the rebirth of Juno. She then played a small role in Assassin's Creed Syndicate through the WWI eyes of Lydia Frye, the granddaughter of Jacob Frye.
That's not the most notable relation in AC Syndicate, however. There is a journal entry that surprisingly reveals that Desmond had an illegitimate son named Elijah (pictured below), and he was also ironically a Sage. She was also notably looking through Helix archives in AC Rogue and the positively-review bombed AC Unity, though the reasoning is never confirmed. After this, beyond any small mentions such as Odyssey's latest DLC, Juno disappears from Assassin's Creed. This is because her storyline was relegated to the comic books, spurring a series known as Assassin's Creed Uprising.
Assassin's Creed Uprising revolves around Elijah, Juno, a piece of Eden known as the Koh-i-Noor, and the Instruments of the First Will. Uprising's first issue released in February 2017, 8 months before Assassin's Creed Origins came out, but didn't wrap until midway through 2018.
AC Uprising focuses on the story of Charlotte De La Cruz, a modern-day Assassin who also witnesses the memories of her Spanish Civil War-era ancestor, Ignacio Cardona. He ends up taking up a temporary truce with the Black Cross of the Templar Order, a member tasked with internal investigations into corruption. This is because of the Instruments of the First Will, a cult devoted to Juno who would recruit members from both sides, as well as manipulated both sides.
This is paralleled in the modern story where Juhani Otso Berg became the Black Cross. He and Charlotte take up a temporary truce in order to defeat the Instruments of the First Will, who are seeking the Koh-i-Noor. This Piece of Eden is arguably the most powerful introduced in the AC franchsie yet, as it can locate other Pieces of Eden and bind their powers together.
Throughout all this, the Instruments of the First Will manage to use the Shroud of Eden and Elijah's DNA to give Juno a real body. It is put through an accelerated growth process, giving her a brand new body and Isu powers within 24 hours. However, as she emerges, Desmond's son, Elijah, betrays her.
Once Juno realizes this and demands Elijah to hand over the Koh-i-Noor, Charlotte manages to assassinate Juno, effectively ending her storyline. Elijah then disappears with the Koh-i-Noor and hasn't reportedly been seen since. It'll be interesting to see if Elijah and the Koh-i-Noor find their way into the games, perhaps in Assassin's Creed 2020, but many are conflicted over this ending for Juno.
Many who are even aware this has happened dislike how a major story arc introduced in the games was subsequently wrapped up in a comic book series. However, with the major changes that took place with the franchise in AC Origins and AC Odyssey, this isn't that surprising. Many also think this, as well as her actual end, undermine the threat she faced to the world.
The complaints are certainly justifiable to a degree, but as it stands, it seems the Assassin's Creed franchise is about looking toward the future, not the past — at least from a design perspective.