The Clone Wars: Act on Instinct was written by Pablo Hidalgo. The art of the comic was done by Thomas Hodges, Grant Gould, Jeffery Carlisle, and Daniel Falconer. Special thanks were given to Sue Rostoni, Leland Chee, and Dave Filoni.
The comic starts out with Jedi Master Bolla Ropal discussing the Republic seeking to put a base on Devaron with politicians from Devaron. Ropal assures the politicians that the Force would turn their valley lush and green. He is more worried about "fortifying the future than wage war in the present."
Meanwhile, clone troopers under Commander Ganch are working to block a river. Jedi Padawan Tyzen Xebec repels down on a rope when he hears the clones complaining about their work. Suddenly, an alarm sounds, warning Ropal, Ganch, and Tyzen to an enemy task force entering the system. Cad Bane, who is leading the force, orders the land assault to begin. He also speaks to Aurra Sing, whom he orders to distract the Padawan and the clones while he goes for Ropal. Aurra orders her battle droids to open fire on the clones' gunship. The gunship explodes, causing Tyzen and Ganch to become pinned down under wreckage.
Cad Bane and his land assault force attack the remaining clones, and moves in to capture Ropal. Aurra targets Tyzen, who is still trapped in debris with Ganch. Ropal orders Tyzen to stay back, as Cad fires a cortosis shot, which not only breaks Cad's blaster, but disrupts Ropal's lightsaber. Cad ties up Ropal with a metallic cord, and demands him to open a holocron. When Ropal refuses, Cad shocks him with electricity through the metallic cord. Cad then takes Ropal away. Ganch contacts Anakin Skywalker, and fills him in on the events. Before Anakin can get any answers from the clone, he is attacked by battle droids.
Planetside, Tyzen orders the clones to open fire on the braces of the dam holding back the river. The clones seal up their helmets, and destroy the braces. The river floods in and wipes out the droid attack force. Ganch and Tyzen climb out, and Tyzen worries about Ropal. He sits beside the river, feeling sorry that Ropal never saw his creation for the Devaronians, and awaits the Republic gunships coming to rescue him.
Back at the Jedi Temple, Tyzen is visited by Jedi Master Mace Windu. Windu talks to him, expressing his grief towards Ropal's death. He also tells him, that when the time is right, he will be assigned to another Master. Ahsoka Tano, the Padawan of Jedi Knight Anakin Skywalker sees the depressed Tyzen and wants to cheer him up a bit. She begins a conversation with him, but eventually Tyzen ends up in tears.
Later, Tyzen is assigned to a new Master, just like Windu said. His new Master is the strict Keelyvine Reus. Reus thinks Tyzen to be a loose cannon and tries to teach him patience and respect. Meanwhile, the Jedi Order had ordered the Masters Kit Fisto and Reus to go to the planet Ukio to inspect the planetary shield system. They needed to know if the shield could hold of an attack by the Separatists, because the planet was the main source of food for other planets in the system and for other planets around the Triellus Trade Route and that was why it could not be lost to the CIS.
During the inspection, a single Lucrehulk-class battleship enters the system. Reus suggests to Fisto to make a quick recon, before attacking the vessel. Taking off in their Delta-7B Aethersprite-class light interceptors, the two Jedi see the droid ship launching several modified seismic tanks, which drop a mysterious black cloud in the atmosphere of Ukio. R6-H5 is able to gain a sample as they enter the cloud.
The two Jedi bombard the Separatist ships, but to no use, as the ships continually release the substance into the atmosphere. Upon again trying to contact Admiral Dron, Reus is successful, despite the fact that the enemy was jamming their signal. The admiral tells her that Fisto's sample is being scanned and that they have made some progress. The two generals, upon realizing they are no help to the situation at hand, turned back for the Republic destroyer.
Upon Fisto and Reus's return to the ship, Dron alerts Captain Pharl McQuarrie to prepare to deliver a report on the substance analysis. He confirms the substance to be electrostatic soil from the Moorja Badlands and possessing photoreactive properties. He explains in short that the soil will stick to the shield and remain aligned with the sun at all times, blocking the sunlight crucial to the growth of the crops on the planet used to sustain the Clone Army. The only way to resolve the problem, they realize, is to drop the shields, exactly what the Separatists want. Reus decides that after fifteen minutes, the shields will be partially dropped. She tells Admiral Dron to prepare the fleet in case of a Separatist attack.
Reus and Fisto, each in their own starfighter, lead Blue Squadron in an assault on the Lucrehulk-class battleship and the seismic tanks that are in Ukio's orbit. Upon the squadron's approach towards the ship, it releases a swarm of Vulture Droids in defense. Meanwhile, Ukio opens a hole in its shields to allow for all the soil that had been clinging to the shields and blocking the sun to drift away in the planet's winds. Three CIS Sheathipede-class transport shuttles manage to enter the atmosphere through this hole. One of them is shown landing, and the tactical droid Doctor and a few battle droids carrying some sort of dish exit the ship. Doctor contacts Passel Argente via hologram to inform him that Project Instinction has entered its second phase as a battle droid activates the dish.
A domestic eopie, who had been calmly eating, suddenly breaks out in violence, and an Ukian attempts to wrangle it, but it is no hope. Sanya tells Tyzen she feels a disturbance in the Force, who responds with "I try not to these days"; he then comments on how everything suddenly became so silent. The two turn around to see a group of angry Ukians staring at them, wielding sharp and pointed agricultural tools. Sanya is horror struck, and the Zabrak Padawan responds, now with lightsaber drawn, yelling "Run!"
The Ukian liege asks a worker if the shields are back up. They are reported to be at full strength, and the soil that had been clinging to them has scattered as predicted. He notices that the screen indicates the gigauns have left their normal paths and are headed towards the crop fields. Puzzled by this claim, he orders Ganch to go take a look for himself as the liege believes there must be a mistake since the creatures' actions are an anomaly. Liege now has a crazed look in his eyes, similar to those of the angry Ukian farmers Tyzen and Sanya encountered earlier. His madness increases, realizing the crops were rescued from darkness only to be destroyed by animals. Shouting and demanding answers, he smashes the station the worker had been working at with his staff.
Massive herds of gigauns and flocks of flying creatures head near a group of clone troopers outside the shield generator building. Squawk begins shooting at the animals, only to be caught by Ganch who demands him to drop his weapon. When Squawk refuses, the commander sticks a blaster to Squawk's head, and only then does he respond. Still holding his gun at the unarmed clone, Tyzen steps in, slicing Ganch's blaster in half with his lightsaber. He demands an explanation, but the two soldiers merely approach him as if to attack, and the Padawan again asks them what is happening, this time telling them to step back too. Gasping, Ganch begins to remove his helmet.
Above, the space battle ensues around the enemy ship. Master Reus tries to contact her Padawan, but to no avail. She then realizes the Separatists must have landed on the planet and that they need to be stopped.
Back on Ukio as the chaotic outbreak continues, Sanya advises a concerned Tyzen to step back, but is too late; Ganch knocks the Jedi with his helmet, so strong that he even loses grip of his lightsaber. The now seemingly unstable clone, with the same crazed look in his eyes as those of the eopies and other Ukians, warns Tyzen, "Run before I get my hands on you." Ganch chases the young Jedi through the herds of rampaging gigauns; he catches up, and the two engage in hand-to-hand combat. After the clone draws some of Tyzen's blood by delivering a blow to the face, he leaps from the area of combat into a grassy field where Sanya is. She tells him to focus his actions and to "reach out to the Force." Then his commander arrives and grips the Padawan by the throat. He tries to convince Ganch that something is messing with their heads and causing them not to be themselves. He reminds him of his duty as a soldier and tells him to stand down. Ganch manages to come back to his senses for a moment and uses the opportunity to save Tyzen by knocking himself temporarily unconscious with an injection from a med-shot. Now at his feet and staring down at the unconscious clone, Tyzen excuses him from duty.
Magistrate Passel Argente and his aide Denaria Kee are observing the operation's progress, but he is concerned that things are not going as planned that it was too complex from the beginning. Kee advises him to trust his tactical droid to know what to do.
Tyzen wearily drags the unconscious Ganch from the brush to shelter so he will not be trampled upon by the stampeding herds. Sanya asks him what happened, to which he responds by stating that everything went red, and that all he could feel was the anger he felt when his master, Bolla Ropal, died. He recites a Jedi teaching, and realizes that everything is much clearer to him now that there is peace. It becomes apparent to him that the Separatists are the ones responsible and they must be tracked down and stopped.
Above, the Republic is victorious as V-19s and Jedi Masters Reus and Fisto fly clear of the destroyed battleship, effectively disabling its jamming. Reus is concerned with the situation planetside, as she still has difficulty getting through. She wants to see what is happening for herself and check on her Padawan, Tyzen.
Sanya and Tyzen ambush a group of battle droids guarding some sort of dish, like the one seen with Doctor earlier, next to a Sheathipede-class shuttle. They take out the droids and device successfully, upon which their minds feel much clearer. They can still sense there are two more, and Tyzen plans to take them out as soon as he can. He also tells Sanya he needs her to go check on the shield station and make sure it's safe since everyone around is losing their sanity.
Sanya, riding a STAP, is on her way to the shield station when a battle droid riding another STAP catches up to her. They fire at and destroy each other's vehicles and survive the fall. As the battle droid closes in on her, she reaches out with the Force to her blaster pistol lying nearby and shoots the droid's head off. With her adversary now eliminated, she continues to the shield station on foot.
In the meantime, Tyzen has destroyed the second transmitter and contacts Sanya that he is nearly at the third when a missile destroys his STAP. Tyzen picks himself up and charges the droids guarding the transmitter, cutting through them with his lightsaber and knocking them aside with the Force. Tyzen manages to destroy the last transmitter but is shot just after he does so. Doctor approaches the injured Padawan but is cut down by the newly arrived Keelyvine Reus. The two later rejoin Kit Fisto and Sanya, the former of whom informs them that health checks on the clones and the workers has shown that the effects of the Separatists were temporary. The group is then joined by the just-demoted liege, who informs the Jedi that they and their forces are to leave Ukio immediately.
Elsewhere, Magistrate Argente meets with Count Dooku to tell him that their plan has succeeded and the Commerce Guild has bought most of Ukio's stock. Essentially, the Confederacy of Independent Systems now owns the planet Ukio and its resources.