But why does everyone want to kill Red and Nea? I still don't understand that.
But thanks for the summary! I still don't understand everything, since English is my second language, but at least it makes more sense now. Hopefully, more questions will be answered and the anime will continue sometime. The last season was so beautifully drawn.
Okay so, I went back and checked for you. Apparently Road wasn't the only survivor, Wisely (the guy with the third eye who went into Kanda's memories) was left alive too.
Wisely is probably on our side too, since he was the one who brought Lavi to the Campbell mansion.
Explanation for why everyone hates Nea:
35 years ago, ''a devastating event happened'' and Nea killed every Noah except Road and Wisely.
Wisely decided to put a lock on everyone's memories to protect them but in the chapter where they torture Apo, he removes the lock.
These memories are currently a mystery to us.
The Noah all have inner rage within them but the current incarnations all hate Nea for personal reasons too, like betraying the Earl and killing them.
From what we know, Joyd or ''Tykki Mikk'' is the only incarnation who has affection for Nea.
Apo called it ''obsessive emotions'' referring to Tykki's face looking a lot like Nea, meaning Apo knows about his past even though Tykki doesn't remember it himself.
Everyone loves Mana because he's probably the most similar to the old Earl. Nea is a lot more sinister and fucked up so everyone is aware of the danger he could cause, especially since he could kill almost every Noah and injure Mana.
Cross wanted to kill Red before Nea could revive because he has the potential to kill Mana and could put humanity in danger, we don't know if he has other motivations.
Apo wanted to kill Allen 1.0 because he was Nea's host, and his job is to remove dangerous people related to the Earl.
Currently, it's not 100% clear who will still side with Allen because the cute innocent baby we know and love is permanently gone, and his allies have the potential to hate him since he's not Allen anymore, he's Nea's host.

Story recap so far:
Noahs were all happily living in their world until it got purged by the giant Cross they showed in Allen's Flashback.
They then came into this world to make it theirs. (According to Road, this world was created for this purpose)
Their leader, the Millennium Earl disappeared one day and Katarina D. Campbell (unclear if she knew the Earl personally) found two identical babies where he stood. She decided to raise these babies as siblings, naming them Nea and Mana.
Mana and Nea loved each other but Mana was being haunted by his Earl side, telling him to kill Nea and become the new Earl.
Nea manages to wound Mana and kill 11 out of 13 Noahs, letting Road and Wisely survive for unknown reasons. (It is hinted that they're in cahoots because Road said that Nea fought for Mana's sake and Wisely brought Lavi to the Campbell mansion)
Nea, knowing that his doom is near, decides to seek a host knowing that Mana was gonna kill him. If he has a host, his memories won’t get damanged when he reincarnates.
He stumbles on Allen (1.0) who was a dying soldier. (Unclear why he specifically was chosen since there would be thousands of people dying in that war) He makes a deal with him, Allen will be his host in exchange for him granting Allen’s wish (currently unknown)
After this, Mana manages to find Nea and kills him, shortly going insane himself because even looking at the mirror reminded him of Nea. (presumably, the Earl taking over his mind forced him to die so he can regenerate with a different face and forget about Nea. Mana didn't fight because he was grieving)
While this is going on, the previous Lavi who had white hair was a big fan of Nea and deserted his clan to follow him. He learns that Nea already had a host so he tracks Allen down and they start traveling together.
Apocryphos (probably spelled that wrong) is something like a guardian for Innocence, hunting down Noahs and scouting new vessels for innocence.
He comes across Allen and Lavi (1.0) and decides to kill them before Nea can revive. He uses the Helix of life to consume Allen, breaking him down to his atoms.
The Helix of Life is a principle that every being on this earth has come from and will go to the Helix becase that's where they get their life energy from. The innocence is a parasite that feeds off of the Helix and that's why they work like a duo.
From Apo's explanation, the more life experience, trauma and events someone has, the bigger their Helix is which makes them more suitable targets for innocence.
While Allen was getting consumed, he not only got an innocence but Lavi also jumped in to save him by giving up his Helix instead.
Allen was thrown out after 8 years in the helix and Apo decided that Allen would make a great vessel for the heart because he's back to his child age and Apo can create a lifetime full of trauma to nurture his Helix.
He wipes Allen's memories, gives him to the circus (motivation unclear since he didn't seem to be aware that reincarnated Mana was Also in that circus) and decides to intentionally fuck his life up and create more trauma for him so his Helix can grow more.
After this, MC (currently named Red) starts working in the same circus with reincarnated Mana (who doesn't remember what happened to Nea but he vaguely knows that he has a brother and he misses him)
His reason for joining was because every time the circus performs, the whole town comes to watch the shows and since Mana doesn't remember his brother, he's hoping that his brother can recognize him instead.
Allen was a regular abused child but after meeting Mana and his dog named Allen (unclear if Mana came up with that name himself or he vaguely remembered it because it was Nea's host's name and kept it in his subconscious) He started warming up to them.
Cosimov was a bastard who worked in the circus and was jealous of Mana's success. Apo intentionally mind controls him to mess with Mana so Allen can have more trauma in his life. Eventually Cosimov kills Allen (Mana's dog)
From what we see of Mana, he's currently being haunted by the Earl suit who can sense his grief (unclear if Mana remembers the Noah clan or the Earl)
Red sees that Allen (dog) died and cries for him, somewhat soothing Mana's pain. That day, Mana takes Red out to have fun and they start bonding, not knowing that Apo was currently mind controlling the entire circus to demonize Red
When Red and Mana return to the circus, the ringmaster blames Red for killing Allen even though Cosimov dug him up.
Mana understands that Red didn't do it but Red was so enraged, he activated his innocence to attack them. Mana tries to stop him but Allen hurts him with innocence too which makes his inner noah and hatred for innocence awaken.
Mana awakens as the Millenium Earl and kills the entire circus but Cross Marian manages to stop him at the end. Cross's duty was to kill Red before he became Nea but he decides to spare him because both of his innocence refused to kill Red. (unclear if Apo controlled his innocence himself)
Cross tells him to stay away from Mana so Red decides to bury Allen again and tries to kill himself by staying in the cold. The last panel is Apo standing over him menacingly. (Since Allen doesn't remember his promise to stay away from Mana, we can theorize that Apo erased his memory of Cross so they can stick together again for more trauma)
The next day, Mana is completely GONE, his memory is reduced to atoms and he thinks that Red is his dog Allen who can somehow talk and walk on two legs. From this moment on, Red's name is changed to Allen.
They travel together for a while, Mana teaching Allen all sorts of things, like the writing (lullaby) they created with Mana, his symbols that mean ''I am here'' and his juggling skills so they can earn money.
One morning Mana dies in his sleep and from now on, the story is very unclear.
----------Unclear------------
After Mana dies, The Earl visits Allen and asks if he want to revive Mana but there's no way he can be at both places at the same time.
From what we see in Kanda's perspective, Mana's grave was empty so we don't know who got revived and cursed Allen. Could be the original owner of the body before Mana took over, or could be a small part of Mana's soul who stayed in the body
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After Allen gets cursed and kills Mana, Cross decides to take him as his student and the regular story of the anime starts.
In the second season, Cross Marian was killed by Apo, and his body went missing after the recycled second generation attacked the order.
Latest news:
After Kanda and Johnny left the order to help Allen, general Tiedoll decided to lend them a hand beause his son comes before the order.
Allen told everyone about Apo. Later, he saw Cross in his dreams who instructed him to search for the campbell mansion.
Then the gang decides to split up. Kanda and General Tiedoll head back to the order so Kanda can become a general and look for clues about Mana’s grave .
After searching for a bit, our team discover the Bookman clan who wanted to know what happened to the previous Lavi (White hair)
Allen ingests poison and finally remembers his previous life as soldier Allen, learning that his hair turned White because Lavi’s leftover soul decided to fuse with him.
After learning the truth, the bookman clan leads them to the Campbell mansion where they learn that Cross Marian was actually Cyrus Van Campbell, who’s the ‘’incumbent head of the Campbell Clan’’ meaning he’s Mana and Nea's uncle.
In this chapter, we learn that Allen is simply not the Allen we got to care about all this time, and he's back to his original personality whose virtues and morals are currently unclear.
He heads up to a magically sealed door which was surprizingly used by the presumably dead Cross Marian, or Cyrus Von Campbell.
It is unclear why the Bookman clan is letting Road stay here, probably because they couldn't open the door and didn't know they were staying there.