Over ten years after the first human invasion on Pandora, Chief of the Omaticaya Clan Jake lives
happily at peace with his wife Neytiri and their kids. Neteyam, Lo'ak, and Tuk are their biological
children, but they've also adopted two. There's Kiri, who was born from Grace's comatose avatar,
and Spider, a human boy. Spider had been born on the human military base during the invasion and
cryostasis hadn't been an option for a baby, so he couldn't be taken back to Earth with the others.
Because he was raised by Jake and his family, Spider considers himself more Na'vi than human,
but Neytiri is still wary of him because he's the son of the enemy. One evening, the family looks
up to the sky and is devastated to discover that humans are returning to their planet,
destroying everything on their path as if they hadn't learned their lesson. One year later,
in one of the many human spaceships that are orbiting the planet, the army is transforming
their soldiers' minds into newly hatched avatar bodies. One of them doesn't take his awakening
well until he's explained what's going on: it's Colonel Quaritch, who died during the
first invasion. New Quaritch watches a tape left by himself explaining they copied his memories
into the system so he could be cloned after death, and now his mission is to get revenge on Jake for
defeating them last time. Meanwhile Jake and his clan warriors have organized a guerilla operation
to keep the humans from going far with their plans, mostly by attacking their supply lines.
Most of them use traditional weapons and ride on mountain banshees, but as a former human,
Jake still likes to take guns for his personal use and has adapted human communicators to be used
among his family. During another very successful raid against the humans, Lo'ak gets too cocky and
disobeys Neteyam, jumping into battle to help his dad in order to prove himself. Neteyam goes after
him, and this reckless action causes both kids to end up under fire when a human ship fights back.
Lo'ak jumps out of way just in time, but Neteyam gets hurt and Jake has to rescue him from a pile
of debris. When they return home, Jake scolds his sons for their actions and grounds them. Neytiri
tries to remind her husband not to be so hard on them because they're kids, but Jake he's afraid of
losing them, so he needs to be strict to keep them safe. Sometime later, the siblings go visit Max,
one of the few human scientists that betrayed the military and joined the Pandora defense team. He
and his buddies have a small lab where they keep Grace's comatose body, and Kiri likes visiting
her, she also likes to watch her videologs of when she was still in a human body. Kiri's siblings
tease her for not knowing who her dad is, but Spider thinks maybe not knowing is for the best,
because he hates the fact he's a spawn of the enemy. In the meantime, Quaritch and his team
of avatars land on the new human base in Pandora, where they learn that thanks to their new advances
in technology, humans are settling down at triple the speed compared to a decade ago. Once they get
properly armed, the team goes to explore the forest, where they find machine parts left from
the last invasion, and Quaritch's shocked to see the reminders of his previous body. At the same
time, all of Jake's kids except for Neteyam are in the area having some fun, but they immediately
hide behind the plants when they see the enemy arrive. Lo'ak lets his father know through the
communicator and receives orders to leave quietly, but as soon as the siblings try to move, they're
ambushed by Quaritch and his team. Quaritch immediately can tell these are Jake's kids
because their fingers mark them as half-breed, but the biggest surprise is to see Spider,
who turns out to be Quaritch's son. Since Quaritch and his team now have to wait to be picked up,
this gives Jake and Neytiri the chance to approach them in the darkness after telling Neteyam not to
interfere. Neytiri makes an animal-like sound to alert the children of her presence before she and
Jakes begin killing soldiers from the shadows, and the kids know to immediately bite their captors
and run away. Quaritch recognizes Neytiri's arrows and taunts her to get her location,
but Neteyam decides to join the fight just in time to save his mother. At that moment, a human ship
arrives to pick up Quaritch's team, so Neytiri concentrates on reuniting with her children,
not even thinking about finding Spider as well. This allows Quaritch to take the boy
with him when he escapes. At the human base, Spider is put on an interrogation machine,
but he withstands the pain and doesn't say a word. Quaritch tries the gentle approach instead,
telling the kid he may have Quaritch's memories but he's a different person that would love to
bond with his son, effectively convincing Spider he may not be that bad after all. When the family
returns home, Jake tells Neytiri they should go away. Neytiri refuses to leave her people behind,
but Jake explains Quaritch wants specifically them, so it'll be safer for the clan without
their presence. After Jake chooses a successor, the clan goes through the traditional ritual to
pass off the chief mantle, and the family gets to leave for the Metkayina coast. Here, the local
clans have adapted to the aquatic habitat and can stay longer underwater without breathing.
When the family arrives, chief Tonowari and his wife Ronal are wary of them because of their human
blood and the possibility of the war following them here, but Jake swears they weren't followed,
and since tradition demands shelter to be given to anyone in need, the family gets to stay. Tonowari
asks his children to act as guides, and while his son Aounung wants nothing to do with them,
his daughter Reya gladly shows them around. From then on, Jake's family works hard to adapt to the
reef life, learning things like riding aquatic creatures called ilu and tricks to teach their
bodies to be underwater for longer periods of time. It takes them a few tries to get it right,
but to everyone's surprise, Kiri doesn't need to learn any extra tricks: she naturally can
stay underwater all she wants and she instantly develops a bond with all the creatures of the sea.
Meanwhile Quaritch's team begins taking Spider on their exploring missions, assigning him as their
official interpreter. Spider also takes them to a nest of ikrans, dangerous flying creatures that
can't be tamed by just anyone. Quaritch gives it a try anyway, confronting the creature to
prove himself in combat and accidentally causing them both to fall off the cliff. The team thinks
Quaritch's dead and they're ready to return to base, but at the moment, Quaritch makes a
triumphant return by riding the tamed ikran. Back on the reef, Kiri continues to bond with the sea,
prompting Aonung and his friends to make fun of her for being a weirdo. Lo'ak comes to her defense
and Neteyam quickly follows him to try to keep things diplomatic, but Lo'ak is too hot-headed
and starts a fight anyway, so Neteyam has no choice but to help. When the adults finally come
to pull them apart, Jake scolds his sons for their actions. He's frustrated by the constant teasing
as well, but they have to endure it because they're guests here and they can't afford to
be kicked out. Neytiri tries to comfort Kiri, who is upset over the fact she's different even
biologically, as proven by a section of her face that she keeps hidden under her hair. Afterward,
Lo'ak follows his father's orders and apologizes to Aonung and his friends for the fight. Aonung
accepts the apology and takes Lo'ak to a special remote area to teach him how to fish underwater,
but while Lo'ak is concentrating on his pray, Aonung and his friends leave because this had
been a prank all along. Now Lo'ak's stranded and has to figure out how to come back,
but his thoughts are suddenly interrupted when he's hit by a giant sea predator. Lo'ak quickly
goes underwater to swim away and hide under the coral, but soon he begins running out
of air and has to come out. The predator comes after him as soon as it sees him but suddenly,
a bigger whale-like creature called a tulkun shows up to defeat the predator right as Lo'ak
passes out. Seconds later, Lo'ak wakes up on top of the tulkun, who has saved him from drowning.
Lo'ak befriends the tulkun and as thanks for the help, he removes a harpoon from its fin left
by human whalers. Then the tulkun guides Lo'ak back to the village, although it leaves before
it can be seen. Lo'ak reunites with his family and Tonowari tries to apologize for his son,
but Lo'ak lies and says it was all his idea. This gets him scolded by Jake again, who calls him the
shame of the family. Afterward, Aonung wonders why Lo'ak lied for him, and Lo'ak explains he knows
how much it hurts to disappoint your dad. The next day, Lo'ak tells everyone about his adventure,
and the locals realize that Lo'ak met Payakan, a tulkun that went rogue. Everyone thinks it's
a killer, and they won't listen to Lo'ak when he says Payakan's actually nice. A few hours later,
Lo'ak goes looking for Payakan and asks why it was made an outcast by its own family, but Payakan
refuses to explain. While they swim together as friends, Reya takes Kiri to their clan's Tree of
Souls in order to connect her mind to it and meet Grace's spirit. After a warm hug, Kiri asks why
she's different and who her father is, but before Grace can answer, the connection is lost because
Kiri suddenly has a seizure. Her siblings take her back to the village and Jake calls Max so his team
can take a look at her, but then one that brings her back to consciousness is Ronal thanks to the
use of a traditional medicinal ritual. Max and his doctor friend explain to Jake that Kiri had
an epileptic attack and she shouldn't connect to the tree ever again. Since Max used his own
ship to reach Jake, the signal was picked up by the human base. They lost it when the ship went
further into the sea, and to find it again they'll need someone that knows the area and can help them
visit hundreds of islands. Quaritch takes his team to negotiate with a whaler ship, and when
the whalers refuse to help, Quaritch forces them to collaborate by threatening them with
death. While a pod of tulkuns makes their annual visit to Tonowari's village, Quaritch and his men
reach the first island and capture the locals to demand information on Jake. Spider finally gets
to see how ruthless Quaritch is when interrogation turns violent and the boy has to stop his father
from killing everyone just because they don't know anything. Unfortunately Quaritch still orders his
men to burn all the houses. The news of Quaritch arriving at the islands soon reaches Tonowari,
who warns Jake he's being chased after all. Neytiri wants to go after Quaritch to end
things once and for all, but Jake asks her to be patient and make a proper plan. In the meantime,
Lo'ak goes to visit Payakan while his friends watch from the shadows to see if he's telling
the truth. Lo'ak wants to know why Payakan is an outcast, so the creature opens its mouth and Lo'ak
swims inside to connect his mind to Payakan's. This allows him to see the whole story: it turns
out Payakan's mother was attacked by whalers and Payakan fought back to defend her, but its pod
still kicked Payakan out because they're supposed to be a peaceful species and violence went against
their beliefs. When the kids return to the village, Tonowari and Ronal furiously scold them
for disrespecting tulkun's culture. At the end of the day, only Reya supports Lo'ak and expresses
how proud she is of him. Sometime later, Quaritch realizes that violence won't make the villagers
speak, so he agrees to help the whalers hunt the tulkuns, knowing that killing the creatures the
locals consider their brothers will draw Jake out of hiding. Now Spider has to watch in disgust how
the whalers send up ships to kill the tulkuns with specialized weapons that can track the
creatures' noises. To make matters worse, the only reason they hunt tulkuns is to extract their brain
enzymes in order to use them in anti-aging remedies, and the rest of the creature is
wasted. The whalers throw the bodies back into the ocean and when the villagers find them,
they immediately blame Jake and his family for it. They want to go out and fight back, but Jake
presents them the tracker he found on a tulkun fin and explains is a trap, so for now, they need to
stay put and simply tell the tulkun to swim away for safety. Lo'ak realizes that nobody will warn
Payakan because it's an outcast and he goes to do it himself, ignoring the warnings from his
brother. Neteyam takes his sisters, Aonung, and Reya with him to follow Lo'ak, and they find him
trying to remove a tracker from Payakan's fin. The group jumps in to help, but it's too late:
the tracker has already sent their location to the whaler ship and it's coming for them. The
siblings use their communicators to tell Jake of the incoming danger, and Jake alerts the whole
village, who immediately grabs their weapons and jumps on their ilus to join the fight. The kids
manage to remove the tracker and swim away with it to get the attention off Payakan, but this is
exactly what Quaritch wanted and he sends his men after them. A rather long chase begins underwater,
and since the kids need to stop to breathe, it gives time for the humans to catch up to Lo'ak,
Tuk, and Reya, and they capture them with a net. As soon as Spider sees his siblings being brought
abroad, he tries to fight to rescue them, but he's quickly overpowered by the humans and sent back
inside while the kids are to tied the railing. At that moment, Jake and the rest of the villagers
show up, but they quickly stop themselves from attacking when they realize their kids
are hostages. Quaritch takes Lo'ak's communicator and asks Jake to come alone if he doesn't want to
lose his kids, but as Jake begins to come closer, suddenly Payakan shows up and jumps over the ship
to land on top of it, destroying it with its fins and tail. It also keeps pushing away the
soldiers because the bullets do nothing to it. Now the humans are distracted away from the kids,
Jake calls the others to attack the ship, and the whalers turn around their boats to attack Payakan
with harpoons, causing it to return to the water. A fierce battle begins between Na'vi and humans,
and the Na'vi quickly gain an advantage thanks to their creatures being able to move faster in
the sky and hide underwater. Kiri uses her bond with the sea life to send the plants after the
submarines, and when the main ship begins catching fire after a boat crashes against it, Spider takes
advantage of his position inside to activate the fans and spread the fire all over the vessel;
he also begins to destroy the control panel. The ship eventually comes to a stop and begins filling
with water. Meanwhile Jake is going one-on-one against Quaritch. At first they use their weapons,
but Jake runs out of bullets and sends his ikran to attack Quaritch's, which causes both of them to
fall into the sea. The whalers go after Payakan, shooting a harpoon with a steel rope at its end,
but Payakan does another jump and uses that same rope to destroy the boat. At the main ship,
Neteyam finally manages to come aboard and free his people. The girls jump into the water but
Lo'ak wants to rescue Spider, so Neteyam has to stay to help his brother. At that moment,
one of the soldiers captures Kiri and brings her to the ship to tie her up as well,
thus Tuk convinces Reya to return to rescue her. As soon as they reach the ship though,
Quaritch shows up, pushes Reya back into the water, and captures Tuk as well. The humans are
already leaving the sinking ship, meaning it's easy for Lo'ak and Neteyam to sneak around and
attack them by surprise. As soon as Spider sees them he joins the fight and reunites with his
brothers, but soon they have to run because more soldiers show up, opening fire on them. Neteyam
makes his brothers jump into the water while he holds the soldiers back with his own weapon,
this allows for Reya to show up in her ilu and offer a ride. They wait for Neteyam to join them,
but when their brother finally jumps into the water too, it's revealed that he got wounded
by a bullet. The group immediately takes him to a small island so Jake and Neytiri can look at him,
but unfortunately, Neteyam dies in their arms. At that moment, Quaritch contacts Jake to tell him
he has his daughters and once again asks him to come alone. Jake sends Neytiri away on her banshee
as backup, then returns to the ship with Spider as his guide. Lo'ak is supposed to stay behind,
but once again he disobeys orders and goes back to the ship too. The soldiers are in
position waiting for Jake at the front, but Spider shows Jake how to sneak inside unseen,
giving him the chance to throw a grenade and start a fire. Chaos and confusion follow the explosion,
and this is used by Jake and Neytiri to jump in and begin killing soldiers all over the place.
Neytiri is in berserker mode because of her grief, and it makes Spider too scared to approach her
since he looks like the enemy. Jake manages to reach Tuk and free her, but Kiri is missing - it
turns out Quaritch saw him coming and grabbed Kiri to use as a hostage. This makes Jake drop
his weapons and Spider come out of hiding to beg for Kiri's life, prompting Neytiri to jump in as
well to grab Spider as her own hostage. She wants to trade a child for a child, and when Quaritch
at first says he doesn't care, Neytiri hurts Spider to prove she means it, causing Quaritch to
release Kiri to save his son. Neytiri immediately takes all her children to the water to escape,
but Jake decides to stay behind to fight Quaritch, otherwise he will return with backup. While the
men get into a fierce hand-to-hand battle, the sinking ship goes so deep that it begins turning
around and traps Jake, Quaritch, Neytiri, and Tuk inside. Kiri and Spider manage to stay out,
and when Lo'ak shows up looking for his family, the three of them split to cover more ground.
Kiri uses her bond with the sea creatures to use as guides to find Neytiri and Tuk, and these very
same creatures are the ones to escort them out of the ship. Meanwhile Jake finally puts Quaritch in
a dangerous hold and finishes him, leaving the body to sink into the sea. After fighting so
long underwater he's out of air, but Lo'ak finds him and guides him to a room with some sapce to
breathe as he reminds him of Reya's breathing exercises. Spider is also searching and comes
across Quaritch, who isn't dead, just unconscious. After lots of internal struggling, Spider decides
he can't leave him there and drags his father back to the surface. Payakan also makes a return to
rescue Lo'ak and Jake, this act of heroism finally makes Jake tell Lo'ak he's proud of him. While the
two of them reunite with Neytiri and the girls, Spider leaves Quaritch on an island and watches
his ikran come to the rescue. When Quaritch wakes up, he tries to make Spider escape with him,
but Spider ignores him and jumps back into the water to reunite his family. Sometime later,
the family gives Neteyam a burial following the traditions of Tonowari's clan. Once the
ritual has been properly finished and Neteyam is one with nature, Jake and Neytiri connect their
minds to the Tree of Souls, this way they get to visit Neteyam's soul one last time.