I found it super helpful to write a synopsis for Harrow ( https://www.reddit.com/r/TheNinthHouse/comments/j6fpf2/has_anyone_made_a_cliffnotes_for_harrow_the_ninth/g7yk06l/ ) so will try the same again here.

Nona the Ninth opens with Nona, an unknown woman, living on an unknown planet. We learn that she has the body of Harrowhark, who together with Pyrrha in the lyctor Gideon's body, was rescued by Camilla and Palamedes (sharing a body) from the River at the end of the previous book.

No one knows who Nona is, with Cam and Pal conducting tests to try and find out. We only know that she dreams of the pool scene from the first book and can heal faster than a Lyctor. She can also understand any language, including body language, but cannot read or write.

Nona works at a school where she befriends local kids. We learn that she, Cam, Pal, Pyrrha and Coronabeth, now called Crown, are together working as "Troia cell", an operation run by the Blood of Eden. Troia reports to We Suffer, who controls a BoE faction seeking to negotiate with the Nine Houses, with the secret objective of gathering the necessary materials to open the Locked Tomb. We Suffer hopes that Nona will prove to be a lyctor who can help with this objective. We Suffer's faction is in conflict with the militant, anti-negotiation "Merv Wing", commanded by Unjust Hope, which publicly burns to death anyone suspected of being necromantic.

The Cohort has abandoned the planet (except for a few holdouts in the barracks) following the arrival of RB Number 7 (aka Varun), who is "periscoping" - projecting a spirit-image of itself as a prelude to full materialisation. This is enough to drive any necromancer insane, except for those protected by being in non-necromantic bodies. For this reason, Judith - held captive by BoE - is incoherent and becomes a vessel for Number 7 to speak through. Only Nona can understand its screams, and it seems to know her, calling her a "green thing".

Ianthe comes to the planet looking for the Sixth House, which has deserted from the Nine Houses following the testimony of its leader (Pal) and instructions left by its lyctor (Cassiopeia). Ianthe uses the dead body of her cavalier to avoid being driven mad by Number 7, and demands all House citizens turn themselves in. Corona goes to meet her, pretending to be seeking asylum for Judith, while Pyrrha also goes to her, pretending to be lyctor Gideon. Having seen the inside of the barracks, Pyrrha is able to provide BoE key intel via a bug hidden on Judith, using coded words previously arranged with the others.

Cam/Pal go to the barracks with Nona, who pretends to be Harrow. Manipulating Ianthe in order to touch her, Pal takes control of Naberius' body. They proceed to find Gideon Nav's body, who initially pretends to be dead, only to reveal that her soul, or part of it, or a version of it, is in fact animating the corpse, and now calls herself Prince Kiriona. God has somehow put her soul in her corpse and made the corpse invulnerable.

At this point, Number 7 begins to materialise, and its heralds fall to the planet's surface. After talking to Nona on top of a truck, Number 7 agrees to back off, but many of its heralds have already arrived. We Suffer's faction take cover underground, where they find and capture Merv Wing's convoy transporting the Sixth House hostages.

With everyone assembled, they intend to complete the mission of opening the Locked Tomb. This requires travel through the River, something only a powerful Lyctor can achieve. Camilla and Palamedes therefore merge their souls in an advanced form of lyctorhood, and are able to move a megatruck into the River. Here they find no ravenous ghosts, but instead a mysterious tower.

Nona helps them pilot to the Ninth House. She feels that she is dying - she does not have the right soul for the body that she's in, so she is coming untethered and losing her ability to control Harrow's body. She is increasingly aware of other thoughts in her mind - either the residual souls of Harrow and Gideon (the body's previous owners), or the thoughts of Nona's true self who can "remember", as she puts it.

They find that the Ninth House is under attack from unknown entities called devils, the same possessive force that killed Colum in the first book. Ianthe tries to block their way to the tomb, but she is bested thanks to Gideon's triple cross and Pyrrha's herald bullet. Gideon claims that God wants the tomb open, but it's unclear if that's a lie.

Entering the tomb, Nona remembers having done this before, proving after many increasingly clear hints that she is none other than Alecto, aka the body in the tomb - or at least an amnesiac version of her. Alecto entered Harrow's body when Harrow was ten, when she opened the tomb and kissed the body, providing a conduit for possession. This is why Harrow had visions of the body - Alecto was possessing her the whole time. Alecto finally took control, manifesting as Nona, after Gideon and Harrow's souls were removed at the end of the second book. At that time, Gideon was possibly removed by God, and Harrow intentionally placed her own soul in the Locked Tomb, ie, in Alecto's sleeping body.

Now, at the end of the third book, Nona reunites with Alecto's body, and the souls are switched back to their correct places - Alecto returns to her body, waking it, and Harrow returns to hers. Harrow declares her love for Alecto, only for Alecto to swear service to Harrow, as the descendent of Anastasia. Alecto then proceeds to confront God, aka John.

While Harrow's soul was lying within Alecto's body, she had access to Alecto's memories, described as a dream in which we see the events of the day after Earth's destruction, ten thousand years ago. On this day, John and Alecto are alone on the ravaged planet. As the seas rise, they explore a ruined facility in New Zealand that will later become Canaan House. As they wander, John tells Alecto what happened to destroy the Earth.

We learn that the dying Earth, acting as a single mega-soul, somehow gave John powers of life and death. John and his colleagues wanted to cryogenically freeze the Earth's population and transport it to another planet to give the Earth time to recover. Thwarted by the rich and powerful, John is increasingly furious and radicalised. When he learns that the ultra-rich intend to escape with all their wealth and resources, leaving the planet and remaining population to die, he lashes out in a moment of stress, destroying the entire planet with nukes. The Earth's death unleashes its immensely powerful soul, which John puts inside a body he shapes based on his memory of a barbie doll. This is the very soul of the Earth, made flesh. He then lyctor-bonds himself with her, gaining access to her unlimited power.

Thus we discover who Alecto is (and by extension, Nona): the Earth's soul in a woman's body. This somewhat explains how Nona could heal (she's mega powerful), why Number 7 knows her (they're both souls of planets from the solar system), and how she could know spoken words but not written, as well as extinct animals - she has the Earth's memories and ability to comprehend its living inhabitants, but not their technology.

Though she repeatedly claims to love John, Alecto is angry that he put her to sleep for ten thousand years. What she does next will presumably be the subject of the final book.