Rinoa, Zell, Selphie and Quistis wake up to find themselves in D-District Prison, the place where all political activists are sent. Apparently, some of the SeeDs visited the "dream world" again. Rinoa points out that Zell, who dreamed he was working in a prison, must have been here in the dream and it turns out to be correct.
Normally when someone goes against the President, they are sentenced to death. Since the Witch is now in charge, things have changed. The party worries about Squall and Irvine whose whereabouts are unknown. They are interrupted when a "Mean Guy" comes in to take Rinoa, who leaves willingly.
It turns out Rinoa was getting released because her father, Colonel Caraway, pulled some strings within the military. Irvine was to pick Rinoa (and only Rinoa) up and take her home to Deling City. Rinoa refuses to sit back while Irvine blindly follows orders and jumps out of the car. She would never leave her friends behind! Irvine stops the car and comes out to argue with her.
Rinoa also knows Squall very well. She sighs and shakes her head, explaining that if nobody told Squall to escape, he probably wouldn't. She doesn't care about her father's orders or anyone's orders. Their friends are stuck in an inescapable prison and won't find a way out as easily as Irvine says they can. After kicking, punching, scratching, and then pushing Irvine back in the car, Rinoa finally gets him to drive back with her to help everyone.
Rinoa and Irvine eventually find everyone at the prison after a shootout, where Irvine's skill saves the day. He shows off his gun slinging a bit more until Rinoa kicks and punches him to stop. She is still furious about his earlier reluctance and interrupts him while talking to Squall. Rinoa is relieved to see that Squall was alive since his wound could have been fatal and the prison isn't the best place to recover. However, she doesn't know that Seifer tortured Squall while there.
When they escape, Squall nearly gets killed once again. Rinoa says his fall looked like a very dangerous situation but Squall is outwardly cool and calm. She starts to believe he must be strong and well trained to be unfazed this whole time.
Everyone decides to do something about the Witch's plans to launch missiles at Trabia and Balamb Garden. When Squall doesn't take charge of the situation, Rinoa does (in less-SeeD, more-diplomatic fashion). She suggests that everyone vote on what to do next. Squall eventually splits them into two groups, one to infiltrate the missile base and one to warn Balamb Garden, as they just witnessed missiles launching towards to Trabia. Squall is surprised by Rinoa's resolve since she's an outsider who is risking her life for them. Wanting to be treated like an equal, Rinoa offers to go on any team.
While Selphie's group infiltrates the base, Squall's group finds that Balamb Garden is in chaos. The students are split into two factions, one following Headmaster Cid and the other following someone called Garden Master Norg. They are fighting each other, the Garden Faculties and monsters from the Training Center which were let loose by Norg.
With Xu's help, the party finds Headmaster Cid who then explains a plan to save Balamb Garden from missiles. Cid planned to stay and die at Balamb Garden but Rinoa refused to let him do that, a place can always be rebuilt but people cannot. Squall shared the same feelings, as Balamb Garden means a lot to him, too, but says nothing.
Following Cid's suggestion, Squall's group heads to the MD level where they look for a control system. On the way, Squall once again nearly looes his life by climbing an unstable ladder. Rinoa is shocked but Squall brushes it off as just a little scary. She believes he must be really brave.
Out of luck and ideas, Squall turns a valve on a whim and it causes the Garden to become mobile. Now that they have avoided the missiles, students realize that there are bigger things to worry about and the fighting subsides.
The garden is moving but nobody knows what to do. Again, luckily Squall tries to steer the flying Garden, saving it from crashing into Balamb town. They then leave Garden drifting on the water until someone can figure out how to maneuver it.
Back at the Missile Base, Selphie's team has done all they can. Failing the mission and having set the base to self destruct, they think about the end of their lives while they are trapped inside.
Now that things at Garden are slowly coming back to normal, Squall thinks about what has happened to Selphie's party. He worries about having ordering them to uncertain death and what they will think of him. He also wonders what the Witch's plan is in all this and about Seifer. He drifts off to sleep, since he thinks too hard whenever he's bored.
A while later, Rinoa somehow gets herself into Squall's dormitory and finds him in bed. She watches him until he wakes up and then cheerfully greets him with a weird phrase. He isn't happy about the intrusion or her jokes about how cute he looked and covers his face in annoyance. However, he doesn't tell her to leave his room.
Rinoa wants him to give her a tour of Balamb Garden and he asks if it's one of her ridiculous orders. She says she just wanted a tour of his home and he eventually gives in. All the students can be seen getting back to normal, many are reminiscing or enjoying the moment and the ocean view. However, Squall gives Rinoa a rather straight forward tour, which Rinoa finds amusing because it's just like him to give her a serious tour. Rinoa and Squall spend the time teasing each other for their contrasting personalities.
The only place Squall was morbidly enthusiastic about was the Training Center and Rinoa could just see him taking someone for a first date there. When they pass the Infirmary, Kadowaki jokes about Squall having never been seen with a girl before and that this must be his girlfriend. Rinoa wants him to play along but he's uninterested, he simply does whatever Rinoa tells him to do (much to her chagrin, she was serious about wanting to be his girlfriend). Rinoa decides to split with Squall for a while when they reach the library as the books interest her.
Squall and Rinoa are then summoned to the "Master's Room" in the basement of Garden and they meet Norg, the greedy proprietor of Garden arguing with Cid. Cid leaves and Squall is (internally) shocked to learn that Norg isn't human, that his orders were false and that Cid and Witch Edea are a married couple. Siding with Cid, Squall's party fights against Norg. After they defeat Norg, Squall has a minor breakdown over the information he has just learnt. He says to forget about it but Rinoa disagrees, wanting to comfort him. They decide to talk to Headmaster Cid to figure out what is going on.
They find Cid crying in the Infirmary and he explains the truth behind SeeD, Norg and the Witch who is also his wife. Garden was created to raise SeeDs who would defeat the Witch. Cid's wife, Edea was aware that they may one day need to fight her but Cid didn't think it would ever happen.
In order to fund Garden, they needed help from Norg of the Shumi tribe. Norg wasn't a normal Shumi and was money hungry. One of Norg's ideas was to deploy SeeD mercenaries for money and it worked, however the ideals behind Garden became lost. After their conversation, Squall remembers that they need to find a way to stop B-Garden from drifting along. For the meantime, the party leaves Cid alone.
A ship with White SeeDs board B-Garden asking for Ellone to come with them and Cid agrees, saying that it's safer that way. Squall is then ordered to find Ellone. Rinoa asks who Ellone is but Squall only tells her it's someone from the "dream world". Rinoa then tries to find Ellone anyway.
Later that day Squall tries to sleep but with so many unanswered questions he finds himself full of doubt. Rinoa once again comes by his room and catches him talking to himself. After a bit of joking around about catching him in the middle of an embarrassing moment, she invites him for a walk, to cheer him up and he gives in.
Just as their 'date' was about to start, Headmaster Cid is back on the announcement system as the lines are fixed but is interrupted as Garden crashes into Fisherman's Horizon. Squall and his party at Balamb Garden are then ordered by Cid to make introductions and apologies to the Mayor of FH. On their way there, Squall wonders why Cid is acting strangely and why Cid is ordering specifically him to do the job. Still, he doesn't question the orders.
The town of FH is a peace-loving one, full of drifters from all over the world. Many people who couldn't find their purpose in life seem to have washed up here, as Balamb Garden just did. The inhabitants enjoy fixing things and some are familiar with Balamb Garden as they have worked on it before.
One of the familiar faces there shrugs Squall off, causing Squall to notice that both the man and himself don't sound very nice. Before finding the Mayor, the party finds (ex)Headmaster Martine who has been banished from Galbadia Garden but is now starting a new life thanks to the people of FH's help. After Vinzer Deling was killed, Galbadia and G-Garden were completely under Witch Edea's control, just like the previous Witch War. Colonel Caraway was also dismissed when Edea rose to power, as there were suspicions of him being involved with the assassination attempt.
They reach Mayor Dobe, who offers FH's help in fixing and operating Garden, so that it can leave as soon as possible. Rinoa, much to Squall's annoyance, questions the need for them to leave so soon and Mayor Dobe answers that Garden isn't welcome because it's a military organization that uses violence to settle problems, something against their beliefs. Since violence attracts violence, they don't want Garden's presence. Dobe's wife, Flo says that they believe any problem can be settled by discussion. If everyone can reach a mutual understanding there is no need to fight.
Just as Squall and his party leaves, Galbadian soldiers who strangely are searching for Ellone invade FH. Dobe tries to reason with them but gets nowhere. The party fights the soldiers off and then the BGH251F2 from the Missile Base to find Selphie's group inside! Turns out they survived by staying inside of its armor and the battle occurred because they were pressing buttons to get out.
Squall is extremely happy to see everyone alive and Rinoa takes notice of this huge change in him. As soon as they're alone, she points out how surprisingly sweet and honest he seemed just then, caring about his friends. She asks how he would have felt if she was part of that team and it makes him blush when he tries to answer. Before he can say anything, she calls him cute for taking the question so seriously.
If Rinoa was in the missile base team Squall can admit to missing her as well and she punches at him. As well, if Quistis was in the garden team, she can have tea with Squall.
Selphie, however, is still really down because of their failed mission and what happened to Trabia Garden. Irvine plans to cheer her up a little bit and with Squall's approval, Irvine secretly gets FH's people to fix the stage.