- "We will let the Jedi Generals know that we will fight to be free! We will fight to defend our planet! We will send the Jedi home in caskets!"
- ―Alto Stratus
At first the Republic had the upper hand but they stretched themselves too far and the separatists, led by Alto Stratus and Dark Jedi Asajj Ventress, quickly gained the upper hand. Suffering heavy losses and pursued by the Separatists, the remaining Republic forces retreated to the southern hemisphere of the planet.
Only the valiant last stand of a quickly formed battle group of clone troopers and Jedi Padawans prevented a total rout by tying up large Separatist forces for several days in the battle of Cobalt Station, buying the remnants of the Republic task force enough time to evacuate off the planet.
Republic agents have described war on Jabiim as "inevitable" and that Jabiimi Nationalist Alto Stratus, a folk hero among his people known for strong anti-republic speeches led a coup against his planet's pro republic congress. He was succesful in this, but many believed that he was bought out the CIS's promises of military support and credits for his faction. However, few of the pro-republics of the congress survived under the leadership of capt. Orliss Gillmunn. The nationalists and the royalist then became engaged in a civil war.
After that, Jabiim rejected republic negotiations from the Alderaanian Diplomatic Corps. Rather than lose Jabiim and its valuable mines, the Republic decided to retake the world by force. The Republic positioned their strike force on nearby Handooine. 
In the first montht, the republic forces under Kenobi and the loyalists had the upper hand. In reality though, this was actually part of a Separatist strategy to divide the Republic forces. Stratus kept his battle droids and his elite Nimbus commandos in reserve for a strike on the now-vulnerable Shelter Base. He attacked on day 21 after the Republic landing, inflicting heavy casualties, including two Jedi generals and most of the Padawans present. Kenobi and his ARC trooper was thought to have perished. However, it was later revealed that he had survived; he and the ARC trooper had been captured by the Dark Jedi Asajj Ventress and transported to Rattatak.
The Republic was ill-prepared for the atrocious conditions on Jabiim, whereas the Jabiimi rebels had lived there all their lives. The task force's heavy equipment became mired in the muddy, rain-soaked plains, where they were vulnerable to the agile Nimbus commandos, while the constant storms and heavy raining severely impeded their much-needed orbital and air support. Even Republic radio communications and sensors were scrambled by the turbulent atmospheric conditions. Thus the rebels could time and again defeat the Republic despite its superior numbers and firepower.Over the course of the next week, Stratus's forces made significant gains in the northern hemisphere, defeating General Norcuna and wiping out his forces at Choal. By the end of the 1st month after the first landing, 18 Jedi and over 9,000 clone troopers had been killed in action. General Leska, now the highest-ranking Jedi on the planet, ordered an immediate strike at the Razor Coast in an attempt to capture Stratus. The Republic defeated the Separatist forces there, but suffered heavy casualties, and Stratus was nowhere to be found.
Stratus had actually escaped and personally led an attack by the elite Nimbus soldiers on a supply convoy led by Commander Skywalker, which was carrying much-needed reinforcements and material to the Republic base at Cobalt Station. The convoy was led into a minefield, which neutralized most of its armored support. The Jedi were unprepared for this sort of ambush, as it was the first time the Confederacy used mines in combat, a disturbing development, and suffered heavy losses. The Republic force was eventually able to break through thanks to the Jedi, who used the Force to detonate some of the mines, distracting the Jabiimi and clearing a path out. Stratus himself was injured in the battle, but only lightly, and vowed revenge. He now gathered his forces for a final, decisive attack on Cobalt Station, the Republic's last major defensive installation on the planet.
On day 37, Leska was killed in action and her task force defeated, and Commander Skywalker assumed command. The last survivors of the Republic forces were in disarray and left leaderless, however, and a full-scale evacuation was planned. Meanwhile, the Jabiimi Separatists, now reinforced by strong Droid Army contingents, were advancing on the departure point at Monsoon Mesa, just south of Cobalt Station. A small group of young jedi and clones held out for five days against an army of more than 10,000. Stratus was killed in the last hours of the battle by Aubrie Wyn, a young commander, and half of his forces destroyed, although Republic casualties were also heavy. Every Jedi present died, except for Skywalker, who—on Chancellor Palpatine's orders—had departed to lead the evacuation. However, the battle group had succeeded in delaying the Separatists long enough for the main Republic force to be evacuated off the planet, and Stratus' death made any organized pursuit impossible.
On day 43, the Republic started their evacuation. Unfortunately, there were not enough ships for both the clones and the remaining pro-Republic loyalist forces, who were desperate to escape the revenge of the now successful Separatists. Skywalker chose the clones; the Loyalists were abandoned to their fate with the words, "This is your war now." The Jabiimi, who had placed their trust in the Republic, rightly felt betrayed and tried to force their way onto the ships, but were repulsed by Skywalker, who held them back with the Force Choke Force technique. Left behind watching their one hope of survival deserting them, they threw mud and curses at the retreating Republic forces.
The planet was lost to the Confederacy, so although both sides suffered severe casualties, the battle was considered a grievous defeat for the Republic. It left a legacy of enduring hatred among the Jabiimi people of the Republic that had betrayed them in their hour of need, the Jedi, and most of all the name of the betrayer Skywalker. Also, while the Republic lost 27 Jedi and over 6,000 clones, with two of three evacuation transports damaged, as well as seven walkers lost, the Separatists lost over 8,000 Nationalist soldiers, huge numbers of their battle droids, many Nimbus Commandos, and every last assassin droid deployed on the planet.