I am obviously not going to include all the missions here (or even most of them). Only the ones relevant to the story and the main characters will be listed.

• Marche Radiuju, the new kid on the block in the city of St. Ivalice, is having his first day at school, where apparently the curriculum consists of a snowball fight. Most of the kids pick on Mewt Randell, a rather sullen youngster; however, a spunky girl named Ritz Malheur berates them.
• Mewt tells Marche he's planning on buying a book. Marche, however, has to go home to meet his invalid brother Doned, who's coming out of the hospital. Marche invites Mewt and Ritz to come over to his house afterwards to look at Mewt's book.
• On the way home they meet Mewt's father, Cid, being accosted by his boss. He's a pretty pathetic sight (having lost his wife, Remedi, sometime earlier and never really recovering).
• That evening, Marche, Ritz, Mewt, and Doned pore over the book Mewt brings home, and talk about how nice it would be to make a video game come to life.
• The spell in the book activates during the night, turning St. Ivalice into the country of Ivalice, a fantasy world populated by humans, moogles, bangaa, nu mou, and viera. Marche is deposited smack into the heart of the city of Cyril, where he bumps into a nasty bangaa. He's saved by a moogle named Montblanc, and has his first engagement (battle) right there. He also finds out about Laws.
• Montblanc takes Marche to the Cyril pub, where he's introduced to Montblanc's clan. Marche decides to join them, having nothing better to do in his quest to find out what happened and how to get home.
• After doing a bunch of missions from the pub, Marche eventually catches up to Ritz in Nubswood. She's also joined a clan - this one's all-viera (and Ritz herself has viera job commands). After a battle against the Cheetah clan, Ritz introduces Marche to her new viera buddy Shara. Ritz has figured out what happened, but has decided she doesn't want to go back to the real world, mainly because in that world she has to continually dye her naturally white hair, whereas in the new one she's a natural pink.
• The next story mission takes place in Eluut Sands, where Montblanc informs Marche of a rumor of five Crystals, which alter monsters' minds.
• The next one is in Ulei River. Marche is sent to investigate, and finds himself warped to a strange place which houses a large Crystal. Upon approaching it, however, a Totema (guardian) named Famfrit comes out of it and attacks Marche! Marche defeats it, the Crystal is destroyed, and Famfrit allows himself to be summoned by the Moogles in Marche's clan. Marche sees a brief vision of Mewt after destroying the Crystal.
• We now discover what happened to Mewt - he's in Bervenia Palace, and is now Prince Mewt. His father Cid is the Judgemaster, and his deceased mother is now Queen Remedi. The wacky Laws are all the prince's doing.
• Marche next visits the city of Cadoan, where he hears about a character named Ezel Berbier who's concocting a way to fight the Laws. Marche soon meets up with him being pursued by units from the palace. Marche protects him, but Judgemaster Cid shows up and immobilizes Ezel with a Law. However, Ezel demonstrates his Antilaw cards, which remove the Law and teleport Ezel and Marche out of there. Ezel sets up a secret Law Card shop in Cadoan for Marche's use afterwards.
• More missions, then Marche reaches Roda Volcano. Again Marche is warped to a room with a Crystal. This time he fights eight Ultima Crystals, after which the second Crystal explodes and the Ultima totema summon is granted to the nu mou in his party. He then sees another vision of Mewt, who refuses to face facts that his mother is dead, and complains that Marche is trying to destroy his dream.
• The next important mission takes place at Salikawood, where Marche meets up with Babus, Mewt's personal nu mou retainer. Mewt's sent Babus to try to stop Marche from destroying any more Crystals. Marche defeats him, and he escapes.
• Next up is Nargai Cave, home of the third Crystal and its totema, Adrammelech. After it's defeated, it grants the Totema summon to bangaa members of Marche's clan. Babus rushes up to Marche, but sees the vision of Mewt and rushes back to the palace to check on him.
• In Baguba Port, Marche meets with Nono, Montblanc's little brother. Nono's airship was attacked by thieves, who retreated to Jagd Dorsa, a location where Laws have no power. However, the whole "not-dying" deal in the rest of Ivalice also doesn't apply, so it's dangerous. Marche chases the thieves and retrieves Nono's merchandise. A grateful Nono sets up a trade shop in Baguba.
• Marche soon finds out that Bervenia Palace has put a bounty on his head. (Flashbacks of FF Tactics.) The first contenders catch up to Marche in Kudik Peaks, and are quickly dispatched.
• The next mission, involving forged clocks, is in Jeraw Sands. Ritz and Shara again show up having taken the same job as Marche.
• Marche meets with Ezel in the city of Muscadet, who tells him that the judges are on a blitz searching for not only Marche, but anyone associated with him. In Muscadet, a judge is apprehending a moogle just because someone said Marche is traveling with one. Marche takes on the judge's noxious associates and prevails. However, Judgemaster Cid shows up and takes Marche away to prison.
• Marche explains to Cid and Babus about the "real world" and the false one. Before he's done, though, another warp opens up and takes them to the next Crystal. Babus fights Marche alone as Marche destroys the Exodus Flowers protecting the Crystal. After Marche wins, the Crystal is again destroyed and Exodus is given to the viera as a summon. After this, the three see a vision of Mewt and Cid from the "real world". Cid finally wakes up to reality, and tells Marche that he's free to go. He also removes the judges from the power of the palace and declares them to be an independent entity.
• After Cid's leaving the palace, Remedi introduces Mewt to his new protector, Llednar Twem. Llednar is actually an aspect of Mewt - the very nasty one that deals with hurting things badly.
• After fighting off some more bounty hunters, Marche catches a glimpse of Doned in Gotor Sands - but it seems like his brother is trying to get Marche captured! Doned, of course, isn't interested in going back to a wheelchair in the real world.
• In Delia Dunes, Marche meets with Llednar, who tries to stop him. However, a warp opens up to the final Crystal. Llednar attacks Marche, but Cid shows up and uses a special Law that prevents Llednar from using his super-nasty powers against Marche. However, Llednar ignores it, allowing Cid to red-card him and get him out of the way.
• Marche continues to the Crystal room, where he fights the final Totema, Mateus, which then gives itself as a summon to the humans in his party. However, even after destroying all five Crystals, the world of Ivalice remains - because, as Queen Remedi explains, Mewt, Ritz, Doned, and even Marche aren't really interested in going back in their hearts.
• Montblanc tells Marche of Gift Day, a day when everyone goes to the palace to give gifts to the prince. Marche sees this as the perfect way to get ahold of Mewt and convince him to go home. However, first Marche has to find a present. Montblanc says Nono can come up with a great gift if Marche can find some Materite.
• Marche searches for the Materite in the Materiwood. However, Doned again tattles on him, with another clan attacking him. After the battle, Doned steals the Materite and runs off.
• Nono manages to whip something up anyway, and while Marche and Montblanc make it fairly far into the palace, they're then ambushed. Babus saves Marche from the rest of the guards, though, and takes him to Mewt. Marche fails to convince Mewt not to listen to Queen Remedi, and Llednar then appears and attacks. Babus sends for Cid, who again arrives and gets rid of Llednar.
• Mewt and Remedi run away to a place called Ambervale, where Remedi apparently hopes Marche won't be able to find them.
• Marche also needs to convince Doned, so he places a bogus mission at the pub designed to coax Doned out of hiding. In Tubola Cave, he finally meets up with Doned. Marche tells Doned that while Doned was an invalid, that resulted in his continually getting their mother's attention, whereas Marche was always relegated to secondary status. Doned finally apologizes and joins Marche.
• Cid sends a message to Marche to meet him at Deti Plains. After fighting some monsters, Cid informs Marche of Mewt and Remedi's hiding place, but also tells him he'll need some amber from Siena Gorge, with which Ezel can craft a special Antilaw allowing Marche to hurt Llednar. Marche agrees.
• This time, though, the gorge is guarded by Ritz and her clan, who try to stop Marche from continuing. After they lose, though, Ritz agrees to let Marche try to return the world to normal, although she won't help him.
• Marche travels to Ambervale, to be accosted by Llednar. However, this time Cid appears and stops his superpower with Ezel's new Antilaw.
• After defeating Llednar, Marche travels inside the palace at Ambervale to find Remedi and Mewt. After several fights with Remedi and fake Totema she summons, Remedi turns into Li Grim (aka "Le Grimoire"), the personification of the dreams of those who called Ivalice into being. After her defeat, Mewt finally wakes up to the truth. Ivalice begins to revert back to St. Ivalice.
• While it's happening, Ritz and Shara have one last talk where Shara claims that white hair is beautiful and a sign of honor among the viera. Ritz takes the hint, and back in the real world, leaves her hair white. Cid meets Biggs, an old employee of his, who has a new prospect for him. As to what happened to the country of Ivalice, no one really knows if it disappeared for good or not...

Side Quests:

• Ezel's antilaw crusades culminate in him being a mediator between the resistance and the palace. He asks Marche to come along to help protect him from the rabble who show up protesting the talks. Marche manages to do so, and a treaty is signed whereby the resistance agrees to step down, and the palace agrees to allow limited antilaws and not to persecute former members. Ezel joins Marche's clan in gratitude.
• After finishing the game, many more missions open up. Apparently Mewt and Remedi are still gone, but everyone else, including Marche, Ritz, Doned, and Cid, remain in Ivalice. The game doesn't really explain how that happens.
• A mission is posted about a woman screaming in Tubola Cave. Marche goes to investigate, and it's none other than Shara, who was frightened by antlion larvae. Doned convinces her to join the clan in an effort to get Ritz and Marche to make up.
• Babus posts a mission in an effort to find the teddy bear Mewt left behind (which was originally given to him by his real mother). Marche goes with him to Ambervale, where he meets a ghost of Queen Remedi, whom they fight off. Babus agrees to join Marche's clan after they find the bear.
• Marche finds a mission posted about zombies (actually vampires) in Lutia Pass. Ritz also expresses interest in it, and goes with him there. The zombies have the same names as the bullies from the snowball fight way back from the beginning of the game... so that's where they ended up! After the fight, Ritz also joins the clan and has a rather awkward moment with Marche.

After doing all 300 missions:

• The judges, after the secession from the palace, begin to abuse their power to make ridiculous laws, like "no jumping" or one that requires girls to kiss someone. 8p Judgemaster Cid gets fed up and joins Marche's clan to help stop the judges. They finally stamp out the rogues, but Cid realizes that a clan like Marche's will be required to police the judges from time to time. He also tells Marche that when he retires, Marche would be a good judgemaster. 8-) Credits roll (again).