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, or those part of lengthy side quests with significant story attached.

The ending indicates that this takes place approximately 10-20 years after FFTA, as well as 1-5 years after FFXII:RW. Unfortunately there are other confusing aspects to this, so I will not try to directly integrate the three games.

Several Years Ago (Frimelda Sidequest)

• Frimelda Lotice, the Blademaster, is known throughout Jylland. She travels with her paramour, Luc Sardarc; however, Luc becomes jealous of Frimelda's prowess with the blade and poisons her with Zombie Powder. She becomes a zombie, gradually losing her memories, while Luc takes her sword and leaves.

Present

• Luso Clemens, a perky but ordinary student, is finishing the school year. Unfortunately he gets detention on the last day, and has to report to the library. Once there, he finds a mysterious book which contains a prompt for a hero's name. Luso immediately writes his own, at which point he is thrust into the world of Ivalice.
• Luso lands in the middle of a battlefield. Clan Gully is attacking a giant crushatrice, Klesta. Cid invites Luso to join his clan, as the easiest way to avoid being killed. A judge appears and changes Luso's clothes for him, and they succeed in driving off Klesta. The clan heads to the nearby village of Targ to rest up.
• Clan Gully accepts a mission to drive off wolves which are threatening a chocobo ranch's owner. After the battle, Luso discovers a journal which automatically writes itself as new missions are completed. He is confused and wishes to find out more about it. In the meantime, the clan accepts another mission. Cid says he can do some snooping about the issue in Camoa, but the way is blocked by a band of brigands, the Yellow Wings.
• Luso accepts a mission to defeat the Yellow Wings. After doing so, the clan continues on to Camoa. Cid meets an old friend of his named Ribs, who says that he'll give him information in exchange for a tomato stalk. Clan Gully goes off to fight the monster tomatoes. When they get there, they find that the tomatoes are accompanied by an alraune, whose drill is worth a lot of money. Before they can do anything, a girl named Adelle shows up and says she'll help them in the fight in exchange for some of the profits. However, once the battle's over, she scarpers with the drill.
• Back in Camoa, the tomato stalk buys Cid information about a mage named Lezaford, who might be able to help Luso get back home and explain the mysterious journal - however, Lezaford is believed to have died long ago. Cid and Luso also spot Adelle, who Ribs explains is a treasure hunter who recently accepted a particular mission bill. Clan Gully accepts the same bill in an attempt to chase her down.
• After defeating the Ugohr, a giant turtle, Adelle finally shows up, after letting Gully do all the heavy lifting. However, she falls into a trap Cid and Luso had set up. Unfortunately the drill was already sold and spent. They leave her in the trap and head back to Camoa, only to see her enter the pub after them. She inveigles herself into the clan as they head towards Graszton to find out more about Lezaford.
• In Graszton, Cid meets up with Ewen of Khamja, an old compatriot of his. The meeting ends with Cid injured. He rests up in bed in the inn, and sends Luso to the Aldanna Range, where he's heard that Lezaford still lives.
• After fighting some Mist-infused creatures in the Aldanna Range, Lezaford appears. He takes Luso back to his cottage to discuss the journal. He tells Luso that the journal records his life experiences, and that once it's complete he will return to his home world. The end result is that Luso simply has to experience as much as possible in order to return home. Lezaford also indicates to Adelle that he has something to say to her, but Adelle isn't interested.
• Luso visits Cid, then takes a mission in Zedlei Forest fighting Bombs. Luso is then introduced to Auctions. In the meantime, he learns of a medicine which can be created with Pearl Moss, which is found in the Galerria Deep. Adelle is also interested in the Zingu Pearls found there.
• After defeating the Flowsand Lord in the Deep and retrieving both the moss and the pearls, they return to Cid. Cid is grateful for the medicine.
• Luso takes on the next mission, which is in the Rupie Mountains. However, they meet a mysterious ninja named Ewen, who offers to buy his judge. When Luso refuses, Ewen traps the judge, removing Luso's clan priveleges. After he is defeated, he disappears. Luso finds a stone left behind by Ewen, and the judge reappears. Luso returns to Graszton, where Cid tells him to take the stone to Moorabella to get it appraised. Cid also tells him he should take a trip to the continent of Ordalia, but the airship that flies there is grounded due to a prankster.
• Luso arrives at the airship to see that the prankster is one "Genius Ed", a nu mou sage. However, Vaan, sky pirate extraordinaire, shows up and tries to claim Ed for himself. After some argument, Vaan joins Clan Gully in the battle. After the battle is over, Penelo arrives and chews Vaan out. Before she can drag him away, he lets slip where the next treasure he's after resides, in Tramdine Fens on Ordalia.
• Luso takes the airship to Ordalia (where he is rejoined by Cid) and engages in battle with some ghosts at the Tramdine Fens. After the battle, Luso collapses and has disturbing dreams. After arriving back to town to rest, Cid informs him that a bill has been posted by someone else who is also being disturbed by dreams.
• The clan heads to the Nazan Mines to battle the Oversoul, an undead monster who (guess what?) creates disturbing dreams. Defeating it heals Luso of them. Back in town, Luso, Cid and Adelle are treated by a performance by none other than Hurdy, the moogle from Rabanastre, who's mastered the flute. Hurdy needs a new lute, and posts a bill to ask for help getting it.
• After collecting the ingredients and battling baddies in his way, Luso creates the lute for Hurdy, who decides to join Clan Gully. Cid says that the appraiser from Moorabella has finally come back saying that the appraisal is finished. While Cid and Luso go talk to the appraiser, Illua from Khamja tries to get Adelle to join her group (which she doesn't name). Adelle refuses and Illua leaves. Cid and Luso then come in and tell her that the stone was stolen, and the original owner is looking for it, having posted a bill to that effect.
• When Gully arrives in the Bigsa Greenlands, they discover that they were set up; Khamja ambushes them. After beating them off, they return to town and overhear a conversation about Vaan and Penelo, who are accused of attacking Baron Beltorey. They confront the sky pirates and are told that while they did infiltrate Beltorey's mansion in an attempt to rob him, they were interrupted by Khamja, who were the ones behind the attack on his life. In fact, Vaan and Penelo drove them off.
• When they return to Grazston, Gully finds a bill posted asking for them specifically. When they show up at the Ruins of Delgantua, they find none other than Illua and Ewen of Khamja, who attack them. After staving them off, Illua attacks again, causes a reaction with Luso's journal (actually a grimoire) when it comes close to a grimoire which she also has. This causes Clan Gully to be teleported to Zellea, the Forbidden Land, where they are visited by an image of Lezaford and warned to leave immediately. Before they can, they are attacked by the demon hand of Neukhia, coming through the Rift.
• A gate crystal leads back to Lezaford's cottage. Adelle, troubled by Illua's words, decides to discuss her situation with Lezaford. He tells her that she is one of the "Gifted", a set of special individuals with unique talents, including strength, skill and even nigh-immortality. Adelle is upset by this revelation, though she had an idea of it before.
• Back in town, Hurdy expresses interest in a dig occurring in Goug City. After fighting off "mooglebane", small rabbits which moogles hate, he finds an old instrument he can use. Afterwards, Adelle finally decides to leave the clan to think further on her situation. However, during her wanderings, Illua confronts her again, and hypnotizes her.
• Responding to another bill, Clan Gully comes across Adelle, who is under Illua's control, and attacks them, intending to capture Luso's grimoire. After being brought to her senses, Luso convinces Adelle to rejoin them.
• Back in town, Gully finds a bill purportedly posted by Vaan and Penelo, declaring that they are coming after Lord Eden's jewel called the "Black Cat". Gully chases after them in Camoa, only to find that they're (very bad) fakes; the real Vaan and Penelo help them capture the charlatans, but afterwards they run off with the Black Cat.
• Khamja is finally making their final move; Illua challenges Clan Gully via a posted bill to meet her in the Ruins of Delgantua (again accompanied by Ewen). Illua captures Gully's judge (unless they are in possesion of Ezel's card) and attacks. Luso manages to defeat her, but she warps everybody to Zellea again. Illua is determined to open the Rift by completing her own grimoire first. After one last battle, Illua lies defeated, but not before her grimoire is complete and the Rift opens. Neukhia fully comes through the Rift, and Clan Gully undertakes an epic battle to defeat it for good.
• With Luso's grimoire complete, he finally returns home.

Side Quests - FF12 Characters

Several characters from FF12 can be recruited to your party.

• After meeting the fake Vaan and Penelo, Luso and co. will come across a familiar face in the Fluorgis Aerodrome - Al-Cid Margrace, who tries his trademark charm on Adelle. He'll ask them to take a letter to Vaan, who he'd expected to meet but never showed up. In the meantime, Penelo arrives, and is rather annoyed at Vaan for missing his meeting. She joins your clan as you head to the Ruins of Delgantua.
• In the Ruins, Vaan is under attack by some brigands; after saving him, he also joins your clan. The letter is from Al-Cid to Vaan telling him to go with Clan Gully to fight against Khamja, which was Vaan and Penelo's intent all along.
• A later scene with Vaan, Penelo and Hurdy in Fluorgis references events from FF12RW and mentions other characters back in Rabanastre.
• After Vaan and Penelo join, another mission opens up. Luso had previously accepted missions from a man named Marnot, who kept accepting dates from multiple women at once and asked Gully to fill in for him. At this point, Marnot has concentrated on one woman who has instead taken up with a mysterious suitor. Marnot asks Gully to be his champion in a duel with this suitor, who turns out to be... Al-Cid Margrace, who's collected a bevy of Gria and Viera beauties who aid him. After beating him, Al-Cid asks Luso if he can join his clan in an attempt to get away from his duties as prince of Rozarria.
• Luso accidentally meets up with Montblanc during his main quest when he is accosted by two bangaas who accuse him of thievery. Montblanc saves him from them by finding the allegedly stolen item. Luso thanks him but he leaves before he can ask him his name. Ironically, Hurdy arrives just then and says the moogle Luso describes reminds him of his brother.
• Much later, Montblanc posts a bill saying he is looking for specific treasures. When Luso accepts it, Montblanc is chagrined to find that Luso has already found all of them! Montblanc instead joins the clan, to the joy of his brother.
• Montblanc features in his own side quest, as well, involving a woman named Cois who lures him out to the ruins in an attempt to ambush him rather than for the amorous intent of her quest posting.
• After beating all of the tournaments, the final tournament consists of fighting Clan Centurio from Ranabastre. Fighting them with Vaan, Penelo or Montblanc in your party will trigger extra dialogue.

Side Quests - Frimelda

• Frimelda Lotice, now a zombie, puts up a notice in the pub asking for medicine, not realizing the true nature of her predicament. Luso accepts it; however, the potions hurt her rather than healing her. She asks him if she is dead, and Luso answers in the affirmative.
• Luso later accepts a mission in Fluorgis to get rid of a monster who is terrorizing the city; however, the monster turns out to be Frimelda again, who is simply wandering around.
• Another mission is posted asking Luso to protect his chocobo farm against a Seeq calling himself the Swordking. However, when Luso gets there, he finds a man named Ghi Yelghi, who challenges the Swordking and defeats him; he turns himself into stone afterwards. Ghi indicates he is on a mission to find the Blademaster.
• Luso accepts another mission, from a man complaining of a monster haunting him. As it turns out, it is Luc Sardarc, Frimelda's previous companion, who is being haunted by none other than Frimelda herself in her zombie form. Luc finally realizes that Frimelda isn't dead after all, and cowardly decides to kill her again. She is aided by Luso, and Luc is driven off.
• Ghi Yelghi discovers Frimelda's condition and contacts the Witch of the Fens to create a potion to cure her so that he can fight her at last. She agrees, but at a grave cost - Ghi's own health. He puts up an anonymous mission at the pub which directs Luso to the Nazan mines to retrieve an item to deliver to a "great master of the sword" who is at death's door. Luso doesn't find anyone but some monsters, but does find the potion.
• They deliver it to Frimelda at the Kthilli sands, to find her under attack by monsters, being protected by none other than Luc Sardarc, who regrets his previous actions. They give her the potion, and she returns to human form and joins their clan as a Paladin.
• Ghi Yelghi issues a challenge to Frimelda in the Ruins of Delgantua. He fights her one on one; when Frimelda beats him, he goes to his rest in peace, satisfied that he was able to fight the greatest warrior in Jylland.

Side Quests - Duelhorn

• Luso accepts several missions which pit him against members of Duelhorn, a huge clan from the east which invades Jylland with the intention of converting its clans to be part of Duelhorn itself. They finally meet the four leaders of Duelhorn - Maquis, Alys, the Night Dancer, and Duke Snakeheart - making port in Graszton. They fight them off, but they all disappear.
• A set of missions ensues, involving Luso fighting Duke Snakeheart, Alys, or the Night Dancer in various circumstances. At one point Alys enlists Clan Gully to help her against an enemy clan. Finally, Duke Snakeheart is fed up with the dance of the clans and directly attacks the headquarters of Khamja, which Duelhorn sees as their primary foe. The other three leaders of Duelhorn don't sanction this, causing them to turn against Snakeheart as well as Khamja. Snakeheart tricks Gully into protecting him from his former friends in one mission.
• Khamja contacts Clan Gully and demands to know their relationship to Duelhorn; Alys shows up midway through the meeting, convincing Khamja that Gully and Duelhorn are allies.
• The heads of Duelhorn issue orders to the four Jylland leaders demanding that they immediately attack Khamja strongholds throughout the area, despite the misgivings of Alys and Maquis. Gully finds themselves fighting off Duelhorn's troops to keep the peace. Snakeheart leaks the full plan to Khamja, ensuring Duelhorn's defeat.
• With Duelhorn defeated, Maquis, deluded and obsessed, decides to attack Khamja headquarters himself. Alys implores Gully to stop him. They reach Maquis, but he divides himself into five different people and attacks the clan. Once defeated, Duelhorn effectively ends its campaign in Jylland.
• Maquis, wounded, is taken in by a viera White Mage named Cyda, whose home was destroyed in the war between Duelhorn and Khamja. However, Cyda's health begins to fail - due to being poisoned by Zombie Powder, administered by Duke Snakeheart, who is still bitter at Maquis. Maquis contacts the Witch of the Fens, who says she can make a potion to heal Cyda in exchange for either Maquis's life or his memories. Maquis chooses the latter, and the Witch gives him the Lethean Drought, which slowly erases his memories. However, the drought proves addictive.
• Maquis posts a bill asking for help to find ingredients to make the Lethean Drought. When Clan Gully arrives, he is unable to recognize them, and they are troubled by his intent to further imbibe the dangerous potion. They later find another bill, posted by Cyda, asking them to speak to the Witch of the Fens about Maquis's deal with her, which she has begun to suspect. The Witch explains the history, and tells them that if Maquis continues on this road he will have nothing left of himself.
• Cyda posts another bill, saying Maquis left muttering something about a snake. Gully finally catches up with Maquis, who is facing off with Snakeheart. Snakeheart admits his crimes against Maquis, and Maquis demands payback. Snakeheart is finally defeated for good with Gully's help. Maquis decides to take one last Lethean Drought, despite Clan Gully's warnings.
• Alys and the Night Dancer head back to the Duelhorn headquarters, where they stage a successful coup and take over as leaders. They decide to renounce Duelhorn's expansionist ways and to usher in a new era of peace. They ask Maquis to come with them; however, Cyda enters at that point. Unfortunately, Maquis's memories are entirely gone, and he decides to go back to Duelhorn instead.

Sidequests - Miscellaneous

• Adelle can meet a variety of other members of the Gifted, who confer on her weapons containing their abilities. They include Lennart, who first unlocks her Heritor class, Ljda, Viola, Elpe, Hilo, Nesiaam, and Wermut. They each have their own backstory and reasons for helping her, and some have entrusted their abilities with others who pass them on. Adelle cannot meet the next Gifted before she masters the ability of the previous one.
• Clan Gully is challenges to a set of battles with Cinqueluer - first one on one with each of the "kings", then the entire clan at once. Cinquluer consists of Red King Ruuj, Blue King Bliu, Green King Verre, Black King Nware, and White King Blanch (each of which is a mage of the color indicated).
• The Head Editor of the Bonga Bugle posts requests for help with his monthly publication. Gully finds themselves taking on a variety of duties, from interviews to battles.
• Clan Gully is asked to accompany a Komodo Potion delivery boy throughout his journey to deliver his potions (which he has a tendency to swallow himself). He continually insists he can reach the next point by himself, but always ends up asking Gully for help to continue.
• Chita of Chita's Weaponers posts bills challenging clans to learn weaponry skills from him. Unfortunately he's a bit of a windbag, and his "lessons" are trite and useless. He always ends up challenging Clan Gully to a speed battle.
• House Bowen is intent on defeating the giant Crushatrice Klesta, which killed Bowen's wife years ago. Clan Gully eventually helps them achieve this goal, as well as introducing their latest member, Veis the Assassin, to their ranks. Bowen later meets with Gully as both allies and foes in a variety of missions.
• A rancher in Targ Wood asks Gully to help in catching a variety of colored chocobos in exchange for rewards.
• The Culinary Crusade also enlists Gully to help collect ingredients for various rather odious-sounding dishes; they need to defeat a particular number of specific monsters to complete the task correctly.
• Tournaments take place throughout Jylland; first concentrating on one region (Camoa Cup, Graszton Cup), then a continent (Loar and Ordalia), and finally the Jylland Cup. Each one has a scion-summoning accessory as a reward and consists of three to five rounds. Finally the Champions' Cup is announced, with Gully facing off against Clan Centurio.
• The Nu Mou Nobles and Bangaa Brotherhood have terrorized each other in the Rupie Mountains for ages. Each side enlists Clan Gully against the other side, until both have to band together to fight off none other than House Bowen, hired by a third party. They decide to work together from then on.
• Syrenead Sie Hyskaris, a viera Green Mage, decides to prove herself by defeating a giant wyrm, and enlists Gully's help to do so. She later asks them to help her capture it and then cut off its horn.
• The Jylland Defenders of the Peace ask Gully for help in defeating a variety of marks. The final mark is the Magick Weapon, Upsilon, a giant mechanical contrivance.
• After finishing all 300 missions, "The Final Mission" appears. This is a set of five fights against fearsome enemies, all of whom are Level 99, including the full Cinqueleur and a clan that includes two Master Tonberries. Beating it ends the game again.
• The Brightmoon Tor is a tower that appears near Graszton. It consists of five flights and a boss battle; going from one floor to the next requires examining a special crystal, and there are several paths that can be taken. After completing it once, it will show up in two other areas, each time offering access to different floors. The boss battle in the third area is none other than the nu mou Keeper of the tower; defeating him leads to the final Brightmoon Tor battle, against the giant cockatrice Cerayn.