The Assault on the Tree of Souls was the culminating battle in the struggle between the Resources Development Administration (RDA), and the Na'vi clans on Pandora. It occurred on August 22, 2154 and was an attempt by RDA forces, led by Miles Quaritch, to destroy the Tree of Souls in response to the recruitment drive of the sixth Toruk Makto, Jake Sully, who had in a matter of days gathered over 2,000 Na'vi warriors from fifteen different clans to fight the RDA. Though the RDA routed the Na'vi forces, the unexpected intervention of Pandora's vicious wildlife quickly turned the tide against them and they were overwhelmed, forcing the survivors to retreat to Hell's Gate. The Na'vi quickly regained their strength and pursued them there, forcing the withdrawal of all remaining RDA personnel from Pandora.
Lead-up to the battle
Following his failed attempt to prevent the destruction of Hometree, Jake Sully, with the assistance of Trudy Chacon, escaped from Hell's Gate along with Grace Augustine and Norm Spellman. After making tsaheylu with a great leonopteryx and thus becoming the sixth Toruk Makto, Sully had regained the trust of the homeless Omaticaya clan, which had taken refuge at the Tree of Souls. He asked them if they could save Grace, who was dying from her wounds. The Omaticaya people attempted to perform a consciousness transfer on Grace, but she succumbed to her wounds and died. However, before she died, she told Jake that she was with Eywa.
Enraged by Grace's death, Jake convinced the Omaticaya to fight back against the humans in defense of their culture. Jake sent them to summon more warriors to wage war on the RDA from all the clans across Pandora. Within days he had amassed a force of over 2,000 Na'vi warriors - an action that did not go unnoticed, as RDA satellites noted the activity with growing concern. Colonel Miles Quaritch quickly devised a pre-emptive strike to eliminate Jake and deter the Na'vi from open resistance. This plan involved rigging a Valkyrie shuttle with improvised daisy cutters made from pallets of mining explosives, to be dropped on the Tree of Souls. This awesome demonstration of the RDA's power and the crushing defeat they would inflict on the Na'vi, not to mention the destruction of their culture's heart, would dissuade the natives from further resistance.
The night before the battle, Jake approached the Tree of Souls to ask Eywa for her help in defeating the RDA, pleading with her to examine Grace's memories of urbanized Earth in order to understand that the RDA would do the same to Pandora, but was told by Neytiri that Eywa only assists in the balance of life on Pandora and was unlikely to intervene.
Warned of Quaritch's plans by Dr. Max Patel, Jake prepared to ambush the RDA airfleet; the magnetic vortices of the Hallelujah Mountains rendered scanning and auto-targeting ineffective in addition to the dangers of operating in an unfamiliar environment. However, during the battle, the RDA forces fared well despite being at a disadvantage, easily shooting down countless Na'vi warriors in the air through raw firepower.
Quaritch's air fleet arrived near the Tree of Souls in the early morning, centered around a Valkyrie shuttle loaded with improvised bombs for in-flight deployment and machine gun emplacements on the loading ramp and roof. Escorting the vulnerable shuttle were dozens of Samson transports with gunners and Scorpion gunships and a Dragon Assault Ship, from which Quaritch oversaw the battle.
Jake, riding his great leonopteryx, and Tsu'tey commanded the Na'vi forces, which waited until the RDA fleet came within four kilometers of the Tree of Souls and deployed its ground forces (over a dozen AMP suits deployed from the Dragon Assault Ship and the Valkyrie while hundreds of infantrymen were deployed off the Samsons and the shuttle), before advancing. The Na'vi attacked both - ikran riders, lying in wait on the face of several floating mountains, took the fleet by surprise while hundreds of direhorse riders mounted a frontal charge of the RDA ground forces (which caught the direhorse force by radar first), Norm Spellman's avatar riding alongside them while the RDA infantry and AMP suits formed a firing line, waiting until the Na'vi direhorses were in appropriate firing range. Despite some initial success in destroying several RDA aircraft - primarily due to the element of surprise - the Na'vi forces quickly succumbed to the SecOps' superior firepower. The direhorse riders were cut down and routed by small arms fire with little loss as well as the heavy support from AMP suits, and were broken and pursued by Scorpion gunships providing air support, forcing them on the run. Norm's avatar was also shot during the chaotic retreat.
While more successful, the ikran riders were likewise exterminated; the RDA Scorpion gunships, despite being put at a disadvantage thanks to the flux vortex, were still successful in pursuing the Na'vi warriors and mowing them down with machine guns and rockets while Samson units acted as hovering gun platforms, where SecOps troops poured heavy gunfire upon the ikran riders as well as any attempting to get too close. Tsu'tey made a valiant effort to halt the Valkyrie shuttle's bombing run, boarding it and killing or incapacitating several RDA soldiers before being shot and sent falling to the canopy below. The Na'vi also found it difficult to assault the shuttle, which the machine gun emplacements fought back furiously along with a determined Scorpion and Samson escort attached.
Sully was targeted by Quaritch's Dragon Assault Ship, saved only by the actions of Trudy Chacon, who drew its fire in her Samson. Her transport craft was no match for the military-grade assault ship, however, and after a short game of cat-and-mouse, it was destroyed after Chacon reported her status to Jake and apologized for not being able to do more. Trudy was then killed in the blast when the Dragon launched a final missile to finish her off. Neytiri was also forced to land on the ground when after pursued by a Samson, an AMP suit controlled by Lyle Wainfleet shot her ikran down, right in the midst of the RDA advance.
As the battle turned against the Na'vi, Quaritch ordered the Valkyrie to proceed with its bombing run. Norm Spellman was forced to return to his human body after his avatar sustained gunshot injuries. After recovering from the pain of being shot, he donned an exopack and left the relay module, setting off into the jungle to rejoin the battle. Neytiri, surrounded by advancing RDA troops, prepared to make her final stand, though Jake, flying high above, begged her not to. Seconds before she was about to open fire, the ground began shaking as Wainfleet, detecting large movement ahead of him, ordered the RDA ground forces to halt. He and his men were caught off-guard by herds of hammerhead titanothere and sturmbeest charging directly at their lines. Firing in futility at the creatures' immensely thick frontal armor, Wainfleet and the other AMP operators were wiped out by the ferocious stampede. The surviving human troops were routed, many of them pursued and torn apart by viperwolves. Neytiri realized that Eywa had heard Jake's prayer at the Tree of Souls and had summoned the creatures to aid the Na'vi. A lone thanator emerged, startling her, but did not attack her, and instead offered itself to her as a mount.
Simultaneously, the RDA air fleet was overwhelmed by thousands of ikran, which destroyed most of the escorts and forced the survivors to flee. Some RDA aircraft were boarded by ikran, causing the surviving troops to panic. An embittered Quaritch ordered the Valkyrie shuttle to press the target, hoping to still destroy the Tree of Souls despite the horrific losses. As the shuttle prepared to start its bombing run, it was boarded by Jake who mowed down the crew of a machine-gun nest and threw a grenade into one of the air intakes, before leaping back onto the toruk, destroying an engine and sending the shuttle into a nosedive into the ground, where its unloaded cargo detonated.
After destroying the Valkyrie, Jake attempted to destroy Quaritch's Dragon using the same tactic. However, Quaritch spotted Sully and his riderless toruk, pulling the pilot's yoke to the side and knocking Sully off balance, causing the grenades to miss their target. One grenade bounced off, but the other snagged and detonated on the hull, breeching it and exposing the crew to the toxic atmosphere. Sully, left hanging off a missile launcher, removed a missile from its rack, preparing to throw it into a rotor. Quaritch spotted him and blew an escape hatch to shoot him off with his sidearm, but was too slow to save the ship, shooting at the avatar after he threw it. Sully fell into the jungle, giant leaves breaking his fall, as the out-of-control Dragon floundered and spun groundwards. Quaritch, with his shoulder on fire, quickly entered his AMP and jumped out of the assault ship moments before its unused ordnance detonated in the fires, the wreckage landing behind him on the jungle floor.
Jake & Neytiri vs. Quaritch
An enraged Quaritch searched the jungle, eventually finding the module containing Jake's human body. As he prepared to destroy it, Neytiri, riding the thanator, attacked him. They struggled, and though Quaritch's primary weapon was destroyed, he managed to kill the thanator with his AMP's combat knife, trapping Neytiri underneath it.
Jake intervened as he was just about to kill her, and the two struggled further, with Jake using the AMP's rifle bayonet to deflect Quaritch's blows, eventually breaking his combat knife. He shattered the AMP's visor with the bayonet, forcing Quaritch to eject it and use an exopack. Quaritch taunted Sully, and, with no weapons remaining, attacked the relay module, destroying Norm Spellman's vacant link unit and exposing Jake to the deadly Pandoran atmosphere. Jake attacked Quaritch with his knife, nearly killing him, but collapsed as his human body began to suffocate. Quaritch then picked Jake up with his AMP and prepared to kill him with his own knife, but was shot twice with poisoned arrows by Neytiri, killing him.
Jake exited his avatar Link Unit, desperately reaching for an exopack, but lost consciousness before he could equip it. He was saved by Neytiri, who deduced that Jake's human form was inside the relay module. She found him lying down unconscious and put the exopack he had failed to reach for on his face. Jake began to regain consciousness and fully activated the exopack. Neytiri saw that he was alive and Jake said the traditional Na'vi greeting "I See you". Neytiri began to cry and said the same. This added completely new meaning as this is the first time she saw him in his much weaker human form.
Following the overwhelming defeat of the RDA forces, a mortally wounded Tsu'tey passed on leadership of the Omaticaya to Jake, and the Hell's Gate facility, now lacking mobile defense forces, was overrun by the triumphant Na'vi. The natives, under Jake's supervision, forced the RDA personnel to leave the planet on the remaining Valkyrie shuttle, which presumably ferried them to the ISV Venture Star, which would then take them back to Earth. A few humans, including Norm Spellman and Dr. Max Patel, were allowed to remain on Pandora, and Jake, feeling that Toruk Makto was no longer needed, released his toruk before returning to the Tree of Souls, where the Omaticaya successfully transferred his consciousness into his avatar body permanently.