The War of the Gardens begins very simply, it was time for the field exam for SeeD operatives and Balamb Garden had just signed a contract with the Dollet nation to send several squads to assist them in their current war against the Galbadia Empire. Squall Leonhart, Seifer, Zell, and Selphi took part in this exam. All four were students to one of Garden's newest, and youngest instructor, Quistis. Squall and Zell were placed on Squad B under the command of Seifer, who had taken part in several field exams and failed each time. Squad B's mission was to take control of the central square of Dollet City. Once they accomplished that, they soon grew bored, and contrary to orders, the squad traveled to the nearby abandoned Communications Tower, outside of Dollet City, where they had seen several Galbadia soldiers heading.
The Galbadians had pushed hard into Dollet City and into the surrounding countryside, forcing the Dollet military to retreat into their nearby mountain fortifications. It was then that they called SeeD for assistance, but limited SeeD's operations to recapturing Dollet City only. Squad B soon learned that the Communications Tower was Galbadia's real target, and the SeeD commanders ordered them to retreat. After SeeD withdrew, Dollet signed a peace treaty with Galbadia with the condition that the now reactivated Communication Tower would remain active and under the control of the Galbadia Military.
Seifer was disciplined for disobeying orders and he failed the field exam once again. Squall, Zell, and Selphie (who had been assigned to Squad A), all passed the exam and graduated from Balamb Garden, and all joined the SeeD Mercenary Organization. Their first mission as SeeD operatives was to travel to Timber and assist one of the local resistance cells fight against the occupying Galbadia troops. Squall, Zell, and Selphie traveled to Timber where they meet Rinoa, the leader of the resistance group they were to help. Their first mission was to kidnap the President of Galbadia who was traveling to Timber. They succeeded in taking control of the President's train and escaping with the Presidential Train Car, unfortunately, the President was not onboard and the body double attacked the SeeD operatives.
After their unsuccessful attack against the President's Train, the SeeD operatives returned to Timber and learned that the President has already arrived and was planning to make an announcement at the abandoned TV station. It is important to note that since the end of the war against Esthar, 17 years earlier, no radio communications had worked properly, but Galbadia planned to send a broadcast to the entire world using the Communication Tower outside of Dollet to strengthen the signal. The President announced that his government would be meeting with other nations to create world peace and an end to all wars. During the announcement, Seifer broke into the TV Station and attacked the President of Galbadia. The SeeD operatives raced to the TV station and discovered that Seifer was placed under house arrest at the Garden for violent behavior, but he escaped and left for Timber to help Rinoa, with Quistis chasing after to recapture him. Seifer was kidnapped following the sudden appearance of a Sorceress, and Quistis joined the SeeD operatives. The group retreated from the TV Station, but not before Zell accidentally revealed that they were operatives from Balamb Garden.
After the SeeD operatives escaped Timber, Rinoa's resistance group was dispersed and she decided to travel with the SeeD operatives for a time. The SeeD group went to Galbadia Garden to escape the Galbadia troops trying to find them. Once they arrived there, the Garden's headmaster, Martine, informed them of new orders. Their new orders are to infiltrate Deling, the capitol of the Galbadia Empire, meet General Carroway, one of the highest Generals in the Galbadia Military and assassinate the Sorceress in league with the President. The SeeD operatives, along with one of Galbadia Garden's best sharpshooters, Irvine Kineas, traveled to Deling and met General Carroway. Before the assassination was to take place, the President announced to his people that Sorceress Edea would be his representative at these worldwide peace talks he planned to hold. Just before Edea talked to the gathered crowd, she killed the President of Galbadia and declared herself the ruler of the Galbadia Empire. The assassination attempt by the SeeD operatives failed, but they discovered that Seifer had joined forces with Sorceress Edea as her "Knight." Squall was badly injured during a frontal attack against the Sorceress and all of them were captured by the Galbadia Military.
The SeeD operatives were taken to the D-District Prison for political criminals. But because of General Carroway's political connections and the close relation between the Galbadia Garden and the Galbadia Military, both Rinoa and Irvine were released from prison. Seifer, demanding to know the real purpose of the SeeD Mercenary Organization, tortured Squall until he was nearly dead. Seifer informed Squall that because of the Gardens involvement in the assassination attempt, Sorceress Edea was going to launch missiles to destroy Balamb Garden and Trabia Garden and was going to take personal control over the Galbadia Garden and use it to conquer the world. The other SeeD operatives and Rinoa escaped from their cell and rescued Squall with the help of several Moombas, but they were too late to stop Seifer from leaving.
Squall, now completely recovered, split his group into two parties. Selphie, Quistis, and Zell traveled to the Galbadia Missile Base in order to stop the missiles from being sent to destroy the Gardens. Squall, Rinoa, and Irvine traveled to Balamb Garden to report to Headmaster Cid and begin evacuating the facility. Selphie's group managed to destroy the missile base, but not before the missiles were launched. Squall's group returned to Balamb Garden but discovered that the Garden Faculty were trying to capture Cid and all other SeeD operatives. The Garden faculty was using the monsters from the training center to assist them because most of the students sided with Headmaster Cid when the fighting broke out. Squall soon found out that Norg, the Master of Balamb Garden, had ordered Cid arrested because Cid told all of the students to oppose Sorceress Edea. Norg, who had originally wanted the Sorceress dead, had decided to side with her in order to avoid the destruction of his Garden. In exchange for his survival, Norg was to hand over the SeeDs responsible for the assassination, namely Squall and his group. Norg wanted Cid removed, mainly because he was adamantly opposed to siding with the Sorceress and would therefore threatened Norg's agreement with Sorceress Edea. Squall also refused to allow Norg to take him prisoner and he fought Norg’s special Combat Pod. Norg was defeated by Squall, Rinoa, and Irvine and he entered a cocoon soon after. Members of the Shumi Tribe later came to Balamb Garden to look after the cocoon and punish Norg for his behavior and his greed.
After Norg’s defeat, Cid revealed that Balamb Garden was mobile and the facility narrowly escaped being destroyed by the incoming missiles. Soon after, Balamb Garden was visited by the White SeeDs, who travel by using a magically enhanced sailing ship. After learning about the recent troubles at Balamb Garden, the White SeeDs determined to remove “Ellone” and take her to a safe place. Squall was sent to find Ellone and escorted her to the White SeeDs’ ship. After the White SeeD departed, Headmaster Cid announced to the people in Balamb Garden that, while he would remain in administrative control over the Garden, all military decisions would be handled by Squall, who, against his will, was placed as the new Master of Balamb Garden and head of the SeeD Mercenary Organization.
Completely out of control, Balamb Garden crashed into the Fisherman’s Horizon community on the trans-continental railroad bridge that connected the Galbadia continent with the Balamb Continent. The bridge was built in the years just before the Sorceress Wars and was completed only months before the wars started, as such, it was not used for very long. Fisherman’s Horizon was a city built at the halfway point on the bridge and was to be the primary trading point between the two continents. When the wars started, people began to travel to the community to get away from the conflict. For the last several years, the mayor, a man named Dode, was a former scientist that specialized in energy generation for Esthar. To force the Garden to leave the city quickly, Mayor Dobe sent many skilled workers to the facility to repair the damage and build a steering device to control the ship. The Galbadia Empire attacked Fisherman’s Horizon looking for Ellone. At first Mayor Dobe believed that the situation can be resolved peacefully, but he soon discovered that the Galbadian soldiers have orders to destroy the city whether Ellone is found or not. Mayor Dobe agreed to allow the Garden fight the invaders and the Galbadians are forced to retreat. In a fortunate twist of fate, these Galbadian soldiers are then same ones sent to investigate the destruction of the Missile Base and after capturing Selphie, Zell, and Quistis, they brought the three along as prisoners on their next mission.
With the Galbadians forced to retreat and the Garden repaired, Squall prepared to return to the Balamb Continent to survey the damage, but allowed Selphie to organize the Garden Festival in order to improve morale among the Garden's students. During the festival, Squall discovers that Headmaster Martine is no longer in control of Galbadia Garden and has traveled to Fisherman’s Horizon to find some peace. Squall learns that shortly after Balamb Garden escaped destruction, the Galbadian Military attacked the Galbadian Garden and quickly captured it. They executed most of the Garden Faculty and the mercenaries that refused to swear loyalty to the Sorceress. Leading the executions was Seifer, acting as the Sorceress’s knight. Martine was able to escape with some of his faculty and students with the help of General Carroway, after that they traveled to Fisherman's Horizon to regroup. After the arrival of Balamb Garden, Martine realized that he was no longer fit to lead the students and allowed them to join forces with the students from Balamb Garden.
Squall returned to the Balamb Continent in the fully mobile Balamb Garden and discovered that the Galbadia Garden is also fully mobile and had been moved into the harbor of Balamb, the main city of the continent of Balamb. Sneaking into the city, Squall learns that the Galbadians have “temporarily” occupied the city in their search for Ellone. Leading the Galbadian troops is Raijin and Fuijin, former students from Balamb Garden and close friends of Seifer. The two left Balamb Garden shortly after Seifer went missing and joined forces with him after he had captured Galbadia Garden. Squall and his group defeated Raijin and Fuijin in battle and the Galbadians are forced to retreat from Balamb before they can complete their search for Ellone.
On the advice of Selphie, Squall moves Balamb Garden near the remains of Trabia Garden in order to search for survivors. The missiles had hit Trabia Garden directly and very little of the original building remained, but there were many survivors among the students and the faculty. Unfortunately, the Headmaster and Master of Trabia Garden were killed during the attack, but reconstruction was continuing unabated. During a short rest at Trabia Garden, Squall, Selphie, Zell, and Quistis realize that they had lost some of their memories and only Irvine remembers that they all stayed at the same orphanage when they were younger. Seifer had also been at the orphanage and that the adult in control of it was the Sorceress Edea, but before she became an evil Sorceress. Another person at the orphanage, older than the other children, was a child named Ellone, which is the same Ellone that Squall saw leaving with the White SeeD and that he saw in his visions of the past. Squall and the others determine that the Guardian Forces have made them to lose their memories, which up until then was believed to be a possibility, but had never been proven. They also now believe that it is Ellone that has been responsible for their visions of the past where they were introduced to a former Galbadian solder named Laguna, although the purpose of these visions remained a mystery.
At this point, Squall sent most of the Balamb Garden mercenaries and SeeD operatives into the world to battle the Galbadia Military and only a handful of older students, along with all of the junior students, remained with the Garden. Squall directed Balamb Garden down towards the Centra continent, the former seat of power for the Centra civilization, in order to search for the orphanage where he lived before going to Balamb Garden. On the Centra continent, Galbadia Garden ambushed Balamb Garden and furious fight ensued. Balamb Garden was at a distinct disadvantage because Galbadia Garden was filled with trained soldiers from that Garden and from the Galbadia Military. After defending against two waves of enemy attacks, Squall ordered the Garden to ram into Galbadia Garden, allowing his forces to attack the enemy directly. Squall and his group managed to break through the Galbadia lines of defense and infiltrate the Garden. While there, Squall temporarily disabled the Garden. Squall and his group located Seifer and challenged him to a fight. While Seifer was defeated, Sorceress Edea rescued him, but Squall and his group attacked Edea before she could leave the Garden. During the battle a startling change came over Edea and she stopped fighting and she suddenly seemed to recognize Squall and the others. Before anyone could stop her, Rinoa went to Seifer’s side and teleported him away from Galbadia Garden and then she went into a coma. Squall and the others left Galbadia Garden and the leaderless Galbadians quickly retreated back to the Galbadia Continent in their Garden.
Finally reaching the Orphanage, Squall and his group meet with Cid, and it is revealed that Sorceress Edea is his wife, and together they founded the Balamb Garden, the SeeD Mercenary Organization, and the White SeeD. Edea told Squall that an extremely powerful Sorceress from the future named Utltimecia had possessed her. Ultimecia was using Edea to look for Ellone in order to combine her powers with the powers of the girl. This would result in something Ultimecia referred to as Time Compression, where all time would be compressed into a single moment. Ultimecia wanted to cause Time Compression because at that single moment she would become the most powerful being in the entire universe. Fearing that Ultimecia may now how to locate the White SeeD, Cid and Edea ask Squall to locate them and take Ellone back, so that she can be kept safely aboard Balamb Garden. When the White SeeD are located, Squall learns that they were attacked by the Galbadian fleet and barely managed to escape with the help of several Esthar ships. After being saved, Ellone left the White SeeD and joined the Esthar fleet and returned with them to Esthar.
Abandoning Balamb Garden at Fisherman's Horizon, Squall took the comatose Rinoa and began to travel to Esthar using the Railroad Bridge. On the Esthar continent, Irvine, Zell, Quistis, Selphie, and Edea join him. Edea was traveling to Esthar to learn if Dr. Odine, and expert on Sorceresses and Guardian Forces, could help her prevent Ultimecia from regaining control of her mind and body and the others were escorting her to Dr. Odine's lab. Under the command of Xu and Cid, Balamb Garden traveled across the world to battle the Galbadians under the control of Seifer.
In Esthar, Squall and the others meet with Dr. Odine and they are told to go to the Lunar Gate in order to meet with Ellone. The Lunar Gate is a large structure that is designed to send personnel up to the Lunar Base located at the gravitationally equal point between the planet and the moon. Squall went to the Lunar Base carrying Rinoa and accompanied by Irvine. Zell was ordered by Squall to escort Sorceress Edea back to Esthar for a longer meeting with Dr. Odine. Unfortunately, on the way back to the city, the Lunatic Pandora suddenly appeared and began traveling across the Esthar countryside. Zell quickly returned to the city and learned that the President of Esthar is absent and that Dr. Odine is in charge of defending the city. Dr. Odine told Zell that he believed that the Lunatic Pandora, now under the control of Seifer, will simply pass over the city on their way to Tears’ Point. Unfortunately, with the Lunatic Pandora over Tears’ Point, Seifer can artificially create a Lunar Cry, an event that causes many monsters from the moon to be sent to the planet. Zell, Quistis, and Edea manage to get into the Lunatic Pandora but are thrown off by a powerful machine of Galbadian design. After Zell and his group are kicked off of the Lunatic Pandora, the giant base continued to travel and eventually arrived at Tear’s Point, activating the device.
On the Lunar Station, Squall and Irvine learned that the Esthar President was there to personally inspect the device that is being used to contain the Sorceress Adel, the former rules of Esthar. Squall met with the station commander, a scientist named Piet, and the two agree to place Rinoa in the medical center until Ellone can look at her. The effects of the Lunatic Pandora over Tear’s Point are seen from the Lunar Station as the monsters inhabiting the moon begin to group at a single location on the moon’s surface. A Lunar Cry was beginning and the Lunar Station was in the expected path of the monsters on their journey to the planet's surface. Squall was finally reunited with Ellone and on their way to the medical center, Rinoa awakens and breaks free of the chamber where she had been placed. Several Esthar soldiers are sent to the medical center by Piet to detain Rinoa, but she easily killed them. Squall tried to communicate with Rinoa but she threw him into a bulkhead and continued toward the Control Center of the Lunar Station.
At the Control Center, Rinoa disengaged the complicated seals that were surrounding the Sorceress Adel and then she went to the airlock in order to release the final seals on Adel’s containment device floating in space near the station. After the seals began to turn off, the Esthar President returned to the Lunar Station to discover the cause and Squall got into a space suit in order to chase after Rinoa. The Esthar President prevented Squall from leaving, and after meeting with Piet, he ordered the entire station to be abandoned. Piet, Irvine, Ellone, and Squall are placed on the same escape pod and Ellone sent Squall’s mind back into Rinoa’s past. While there, Squall learns that after Edea was defeated in Galbadia Garden, she lost part of her Sorceress powers and it went into Rinoa, Ultimetia then possessed Rinoa in order to revive Seifer and send him in search of the Lunatic Pandora. With the Lunatic Pandora and Rinoa in place, Ultimetia was able to free Adel and use the Lunar Cry to bring her back to Earth. In space, Rinoa was able to break the final seal around Adel. With her purpose finished, Ultimetia left Rinoa’s mind and leaves her to drift in space. During the Lunar Cry, the Lunar Station was destroyed and the swarm of monsters traveling to the planet brought Adel with them. Returning to the present, Squall used Ellone to communicate with Rinoa only minutes in the past. Squall finally reaches Rinoa’s real mind and she activates the emergency oxygen tank in her space suit. Squall left the escape pod to join Rinoa against the advice of both Irvine and Piet. Squall finally reached Rinoa just as her oxygen began to run out. Squall gave oxygen from his space suit to her, but he believed that there was still no hope for the two of them until he noticed a large ship tumbling in space nearby. The two enter the ship, which is obviously from Esthar, and discovered that there was oxygen onboard. They also learn that monsters had infested the ship killed its crew, and since Adel’s containment device disrupted radio and radar waves, the Esthar Air Station lost track of the ship and believed it was destroyed.
Squall and Rinoa exterminated the monsters and managed to regain control of the ship and return to the planet. After returning to Esthar, the scientists confirmed that Rinoa has inherited all of Edea’s Sorceress powers. Rinoa agreed to be placed in the Sorceress Memorial to prevent her from harming anyone. At first, Squall agreed to let her go, but after he met up with Zell, Selphie, Irvine, and Quistis, Squall changed his mind and took Rinoa from the Sorceress Memorial. Squall took Rinoa to Edea’s orphanage where they learn that Edea became a Sorceress twice in her life, first by pure chance when she was five and then again when she was an adult when she voluntarily inherited another Sorceress’s power in order to protect the children at her orphanage. The power of two Sorceresses’ is what initially attracted the attention of Ultimecia, but even then, Edea was still not as powerful as Adel, which was why Ultimecia left the inheritor of all of Edea’s power, Rinoa, once Adel was free. Returning to Esthar, Squall met the country’s president, who is none other than Laguna Loire, the person that Ellone had sent Squall and the others into the past to watch. Laguna told Squall that after he joined the Esthar resistance group, the people elected him as the country’s new president and he had been in power for the past 17 years.
Laguna and Dr. Odine had devised a plan to permanently defeat Ultimecia, but it would require a great deal of help from Squall and his friends. The plan is to go to the Lunatic Pandora, defeat Adel, and have Rinoa willingly inherit her power, which would make Rinoa the most powerful Sorceress on the planet. Ultimecia would take control of Rinoa in order to give her the power that she needed to achieve Time Compression. Ultimecia's plan was to use her device from the future, which uses a power based off of Ellone's, to take control of both Rinoa and Ellone and then use Ellone to send Rinoa back into the past to actually initiate Time Compression. Based on experience, once Ultimecia had used Ellone to send Rinoa back in time, she would abandon Ellone and this is where Laguna's and Dr. Odine's plan really occurs. Ellone could use her powers to bring Rinoa back from the past after Time Compression begins, and send her, Squall, and his group into the future to confront Ultimecia directly. If Ultimecia is defeated before Time Compression ends, then Dr. Odine believed that everything would return to normal.
To begin the plan, Squall and his group, which included Rinoa, used the Ragnarok to attack and board the Lunatic Pandora. Once onboard, the group is challenged by Raijin and Fuijin, and the two are once again defeated. Afterwards, the group travelled through the base until reaching the control center where they fought one of the Galbadian Military's most powerful creations, followed by a final confrontation with Seifer. Unfortunately, during the confusion near the end of the battle, Adel arrived and captured Rinoa and it was unclear whether Seifer was killed. To complete the next part of the plan, Squall and his group challenged the Sorceress Adel and defeated her, even though she was using Rinoa as a shield. Rinoa inherited all of Adel's power and Ultimecia took control of Rinoa and Ellone in order to begin Time Compression. The last part of the plan was put into motion and after Ellone was released by Ultimecia, she succeeded in sending Squall and his group, including Rinoa, into the future where they directly challenged Ultimecia. After a long and hard battle, Ultimecia was destroyed, and with Ellone's help, Squall, Rinoa, and the rest were brought back to the present and the time stream returned to normal.