Kefka Palazzo is forgotten; as Rufus is occupied and could not even imagine what was about to unfold. 3078; all contact to and from Kalm is suddenly ceased. Kalm being the fastest growing city on the Eastern Continent and under Midgar influence, as they have contacts in Kalm; this is strange. Scarlett orders a squadron to Kalm to check it out. Contact from the squadron ceases as well, right before they last communicated as they were approaching Kalm. Scarlett does not inform Rufus of this, and decides to send scouts and a few choppers to check out the area, and return ASAP. The operation is successful with minor casualties; Kalm appeared to be fortified with AAG (Anti- Aircraft Guns). Everyone assumed this was the looks of yet another mercenary resistance; however the fortifications looked too heavy for a rebel force. The photos taken were examined. The city was overrun with heavily armed soldiers dressed in an odd fashion; bright colored uniforms and armor (Cult of Kefka colors). Also, there was a few machine-like beasts that were guarding entrance/exits to the towns, as well as assumed important points. There were few civilians seen in the pictures. Scarlett did not inform Rufus of this, and instead, ordered a large scale assault on the city of Kalm; with vehicles and all. The fighting lasted for three days, until the ShinRa force was mostly torn apart by the Mako-Tech Armor, and was forced to retreat. Rufus was finally informed, but not by Scarlett. Furious he suspended Scarlett from her duties, and called upon another military commander, as well as Professor Cyrus. For the better part of a month, ShinRa HQ was on lock-down. Rufus ordered Professor Cyrus to build a weapon that could harm this Mako-Tech warrior, as he knew the basics behind it personally; recalling that visit to Junon the year before. He ordered a Combat Alert, and Midgar was basically put on lock-down. Scouting missions were done at least twice a week. Within another month, Cyrus had developed a weapon that could be strapped to assault vehicles that would greatly damage that of the Mako-Tech Armor; the ammunition was fused with pure Mako energy, and was highly unstable. Rufus immediately ordered a 2nd assault on Kalm; however it was strategically attacked opposed to the 1st blitz attack ordered by Scarlett. The battle began the middle of winter, and by Spring, Kalm had been liberated, as the CoK eventually pulled out. Unfortunately, a day or two later, word got to ShinRa that Costa Del Sol, Cosmo Canyon, and North Coral had been captured by the CoK. Reno wakes up at this point, and the Turks, as well as Scarlett and Kazneo at a few points help him recuperate, and bring him up to speed on everything that had happened while he was out.

Rufus was aware that Kefka's base of operations was and always had been at Junon, but he realized that a full-scale attack in Junon was impossible. He required infiltration; covert operations. He called on the Turks. Elena and Rude was forced to leave Reno, who was barely able to stand on his own two feet for a period of time. Rufus figured it was unacceptable. Reno was the leader of the Turks, and therefore he should lead the group into Junon. He could not be reasoned with, especially now with such a threat to his organization, and everything he had built up in the last five years. Kazneo said she was accompanying the Turks to Junon, obviously to get the heat off Reno. Rufus agreed after awhile, and Kazneo was promoted to temporary Leader of the Turks. And they were off. Rufus' next target to assault was the beaches of Costa Del Sol; the highest casualty count in history (aside from Old Midgar being destroyed). It would not be until the end of Fall, before ShinRa managed to gain a foot-hold on Costa.

Meanwhile, Scarlett is now seen to be spending more time with Reno, as she is suspended, and he undergoing recuperation. The Turks managed to slip into Junon, and near Kefka's Tower at the old Junon Capital. The Tower was a new structure, exceeding that of the ShinRa building in height right in the middle of the original Junon Capital. Rude took the identity of a Staff Sergeant, Elena took the identity of some woman in Communications, while Kazneo went all over the place, barley evading authorities and their knowledge of a covert agent in their Capital. Rude was found out and imprisoned as a 'traitor' when he was found snooping around ammunition supplies, and rooting around in classified areas. Elena kept in contact with Rufus himself, and sent him any information that had been passed through her, as well as other important orders given through the Cult's officers. Kazneo met unfortunately with a maniacal Professor Hojo, and was imprisoned without anyone else's knowledge in an experiment cage.

Costa Del Sol had been liberated in late 3078, however the armies were exhausted. Rufus called in a Conscription Law to all males from 16 to 28 to enlist in the SSF (ShinRa Special Forces). There was not much of a resistance to this Law, as the CoK in many eyes, was a complete terror.

Despite the victories of the Military and the new SSF, The CoK seemed to only be getting more persistent and smarter. Nibleheim was captured shortly after the assault began on Costa, and it was without a doubt in Rufus' mind, that Rocket Town would be next. He was correct as the information was passed on to him. Rufus' next move was to set up a fortified base at Rocket Town to stop enemy territory from progressing any further north. The same was done at Gongaga Town in the south. Within the next four months, the military installment at Rocket Town had been completely disarmed. On the flip side, Cosmo Canyon had been liberated fairly quickly; as it was a canyon after all and in ShinRas' favor, and there wasn't a formidable force present. Rufus now saw that the CoKs forces were not massive as his own, and from whoever he was recruiting from (which was from a lot of small towns, and even from Midgar and of course Junon). This was his advantage. By this point, Professor Cyrus had come up with new innovative and improved weapons systems. Infact, recovered destroyed Mako-Tech Armor had been salvaged, and he almost had all the secrets unlocked. It was only a matter of time before they would fight fire with fire. Rufus figured that the war would soon be over.

And then, Sector 8 was completely flattened. It was completely unexpected. Apparently, Kefka (with the assistance of Hojo) had developed some type of super-weapon, which was mounted on top of 'Kefka's Tower' and of course, could not be distinguished from the peak of the building. It was completely Top Secret, and not even Elena could warn Midgar. It was the very first contact between Rufus ShinRa and Kefka Palazzo; right after the destruction of Sector 8. Kefka gloated, and danced around joyfully. He told Rufus that his aiming was off, and if it were not for Professor Hojo's miscalculations, that there would be no more ShinRa, only the Cult. He compared the two, saying that they were not too different from each other. He even went as far to say that if he surrendered, he would not be killed when Midgar and ShinRa were assimilated into the Cult. Rufus wouldn't hear of it, and ordered a full-scale attack on Junon in the summer, something that he had been avoiding from the start. Forces were pulled from the south of the East Continent; however Costa Del Sol remained fortified. Fighting continued throughout the summer. It looked hopeless now for ShinRa, as they gained no ground on Junon. This is when the famed four; Edgar, Sabin, Celes and Locke returned to Midgar, and to Rufus. President ShinRa, being as open minded as possible, decided to hear what these four had to say. They said they could help him, if he were to return the favor. Edgar assured them that they knew how to defeat Kefka, and that it would take strategy over brute force to win the war. They asked about how if he knew how Kefka came into this world, and Rufus had no idea. Edgar said that there must be a strong-energy point on this planet, somewhere strong enough to hold a possible 'Gate' that could bring them back to their home.

Rufus called on Professor Cyrus, which explained to them that there could only be once place to the north; where the crater was. The 'supposive' location to the Promised Land. Celes and Locke thought of a plan. They had to get Kefka out of Junon and to the North Crater somehow. Rufus said it was impossible to drive the madman out of his power seat, which was Junon and his new fancy weapon. Sabin was the one to figure it out, as he pulled a piece of dusted Magicite from one of his claws. Imagine what more power Kefka could derive from Magicite in this world, as it was apparent that 'Materia' was extremely rare these days, as Hojo would have told Kefka already.

Meanwhile, Hojo experimented with Kazneo; as painfully as possible. He didn't try to breed or mutate her, merely torcher her mentally and physically for his own amusement. He kept her updated on the war, however, and explained to her what had happened to Sector 8. He explained that Kefka had a design for such a magnificent weapon, and Hojo merely took the idea and adapted it to this world. It was a device that extracted large amounts of Mako-Energy from the planet, and basically shot the unstable mass of energy at any object, however the weapon was just that, unstable, so he recommended to Kefka not to over-due it. He told Kazneo the stories that Kefka told him. About Gastahl, and his Empire (Kefka came to this land right after Figaro burning, so he wasn't Emperor). Espers, and everything. He told him how he found this world, the location to the North; everything. Hojo was starting to get bored of his new pet, and decided to due away with her. However Kazneo manages to escape, overpower, and kill Hojo in a most brutal fashion. Nearly pushed to insanity, she begins a massacre of any soldier in her path. She breaks Rude out of jail, and the two make their way through the heart of Junon; until they suddenly stopped. They realize they cannot get into Kefka's Tower alone, nor can they escape, so they hide out under the streets, meanwhile the Capital is in chaos at the number of soldiers suddenly dead. Kefka is outraged at Hojo's death, and begins to set up another shot from his super-power weapon. The battle continues just outside Junon with the SSF.

Word is tossed to Elena, still in communications, however she was now promoted to Command. Rufus allowed a transmission to leak about a small rebel band, running around in the North resisting against ShinRa Military; fighting with weapons infused with something called 'Magicite'. Kefka was alerted, and he nearly had a heart attack. He ordered his forces to unleash his most powerful lines of Mako-Tech Armor and soldiers on the SSF outside of Junon, and have them crushed once he returned. Kefka and a small force rushed to the North to Snowy Village.

Edgar, Sabin, Celes and Locke were equipped with Professor Cyrus' new prototype and version of the Mako-Tech Armor; as well they were accompanied by a few dozen ShinRa soldiers, who were to act as the 'rebel force in the North'. Kefka fell right into the trap, and was lead into an ambush right outside Snowy Village. Kefka was maniacal; even more so at this point, and he himself engaged in combat. Edgar and co. was pushed right on the mountain overlooking the North Crater, where close combat continued. Cyrus had explained to them what they must do, and that was to emit a large power force into the 'Gate' which had now grown bigger in mass and size in the center of the crater; it seemed to be engulfing the hole itself. In doing what Cyrus had suggested, supposedly they would be sent home. The remaining 'rebels' dished out all they could to the enemy, until they collapsed. The power-core to their Armor, which was pure Mako- like-contained, was bound together and placed into the four (Edgar, Sabin, Celes and Locke) mechas, and Kefka himself was battered down. He cursed them all; which was much all he could do. The four, now victories, tossed their Mako-Tech Armor (as well as Kefka's modified and more powerful mecha), into the power-source. There was a Big Bang, and they were gone; the entire land mass of the North Crater, and its surrounding (up to Snowy Village) had vanished.

Kefka was gone. The Battle for Junon wasn't looking too bright however. They had received word from surviving soldiers at the North Crater battle that Kefka had abandoned them. The shock value itself could have been enough to diss-illutionalize the troops from continuing to fight, however the High Command realized that if the war was lost, they would be punished severely by ShinRa. They kept it secret, and killed or imprisoned all soldiers who were present at the North Crater Battle. The fighting continued; Elena being very close to the High Command, found this out, but did not dare send it back to ShinRa HQ as she could be killed if caught. Instead, she found Kazneo and Rude, or rather they found her, and she told them what happened. Kazneo knew that the massive weapon which threatened Midgar was useless without Kefka, and his know-how to use it. They were unaware if Kefka taught anyone else the controls, so they figured it was do or die at this point, and infiltrated Kefka's Tower in the center of Junon Capital. They were successful, and assassinated as well as captured most if not all of the High Command. Kefka's Tower had been captured, and the soldiers outside fighting the SSF were unaware; until of course it was announced via Junon HQ communication itself. They were told that Kefka had been destroyed, and that the Capital, the super-weapon had been captured, and the High Command arrested. It took less than one day, the first day of winter 3079, for the Cult of Kefka's surrender at Junon. It only took another day before the CoK's non-violent surrender at Rocket Town, North Corel, and Nibleheim. It was official, as Rufus announced live to Midgar, and the rest of the world who could hear him; the Cult of Kefka had been defeated. The war was over.