Unable or unwilling to submit to imperial rule or assimilate into the other city-states, the Ala Mhigan Resistance wants to fight the Garleans on their own terms, and as such have yet to seek direct aid from the Eorzean Alliance. They are primarily based in the settlement of Little Ala Mhigo in Southern Thanalan.
As Lyse revealed, her father being among its founding members, the Ala Mhigan Resistance was formed to overthrow the mad king Theodoric. When Garlemald conquered Ala Mhigo, Lyse's father was killed as she and her sister fled their homeland for Sharlayan.
Final Fantasy XIV: A Realm Reborn
The Scions of the Seventh Dawn seek the resistance out to investigate the sightings of masked men. After gaining the trust of the Little Ala Mhigo elder Gundobald, the Warrior of Light discovers that several youths in the village are plotting to summon Rhalgr as a primal to combat the Garleans. The plot is halted before they do anything reckless, but limited information on the Ascians is acquired.
In the chaos of the bloody banquet, Yda Hext and Papalymo Totolymo escape the city with the aid of Resistance members to Little Ala Mhigo. They join the Resistance and become involved with a cell called the "Masks". Being led by a fireband called "The Griffin" the Masks claim to have a means to defeat the Empire and inspire many refugees to try to reclaim Ala Mhigo.
Under suspicion of having received stolen shipments of crystals from Ishgard, Alphinaud and the Warrior of Light investigate one of the Griffin's speeches. They reunite with Yda and Papalymo and meet with a proxy speaking on the true Griffin's behalf outside Little Ala Mhigo. The man reveals the crystals were not intended for them, but rather a gift to Amalj'aa so they might summon Ifrit and join the Masks in reclaiming Ala Mhigo.
It is implied this was a feint to ensure the Warrior of Light would confront the Warriors of Darkness at the Bowl of Embers: after meeting with his proxy, the Griffin speaks with Elidibus, who is pleased with the outcome. He presents the Griffin with his end of the bargain: the preserved Eyes of Nidhogg, assuring that as a man of boundless despair and vengeance the Griffin is worthy to inherit them. The Griffin, his true identity being Ilberd Feare, uses the eyes to create a primal by sacrificing his subordinates during their attack on Baelsar's Wall.
Following Ilberd's plot that brought forth Shinryu, the Eorzean Alliance extends an offer of an alliance with the Ala Mhigan Resistance in preparation for a reprisal from the Garlean Empire. With the Scions of the Seventh Dawn acting as intermediaries they meet with a Resistance faction leader, Conrad Kemp. The Scions and the Alliance learn that the Resistance had lost a great deal of strength due to Ilberd's fanatical summoning, losing some of their best fighters. Worse, the Griffin's plot had put the whole resistance under a bad light, making it harder to recruit others to their cause. Despite these setbacks, the Scions aid the Resistance in anything they require, hoping to reinvigorate the members.
To make a show of strength, the Resistance and the Alliance lead a surprise attack against Imperial regulars, aiming to rekindle the spark of hope and bring in more recruits. Though the Resistance and Alliance forces defeat the imperial forces testing new magitek armor, their forces soon face retaliation. Under the command of Fordola rem Lupis and Zenos yae Galvus, the Viceroy of Ala Mhigo himself, the Crania Lupi and XIIth Imperial Legion launch a surprise attack, dealing a grievous blow to the Resistance, critically wounding members of the Scions and defeating the Warrior of Light.
Regrouping after Alliance reinforcements provide support, the Resistance begins to lose hope, with Conrad Kemp believing the fight to be over. Refusing to simply surrender, the Scions continue the fight and, at the Warrior of Light's suggestion, travel to Doma to reignite the flames of rebellion and force Zenos's legion to fight on two fronts, giving the Resistance time to rebuild and a better chance at liberating their home.
After succeeding in reigniting the spark of pride in honor in the Doman masses, gathering other anti-imperial factions, and finding Doma's lost heir, Hien Rijin, the Imperial forces in Doma are routed. The Warrior of Light and the Scions return in triumph as news of Doma's liberation spread like wildfire across Garlean controlled territory, granting the Resistance the chance to renew their campaign to free their homeland with the Alliance's help. The Resistance boldly gains territory from the Garleans, liberating their people, but soon take losses, as after Fordola orders an artillery cannon strike in the middle of a battle at Specula Imperatoris, the blast not only claims the lives of her fellow Skulls, but also of Conrad Kemp. With his dying breath, he names Lyse Hext his successor, encouraging her to lead their people to victory and freedom.
The Scions and Lyse drive Fordola and the remaining Garleans to the capital city of Ala Mhigo, where Zenos also remains. Coordinating with the Alliance, the Resistance handles the populated areas of the city, as they are more likely to trust their own people. As the Resistance handles their mission, the Scions capture Fordola, bringing the Alliance closer to the Royal Palace. After breaching the gates the Warrior of Light confronts Zenos once more, who uses his abilities as a Resonant to merge with the captured primal Shinryu. Despite the primal;s raw power, the Warrior of Light defeats Shinryu and Zenos, who then blissfully commits suicide, finding joy in being defeated by a worthy foe.
With Zenos believed dead, the XIIth Legion retreats, freeing Ala Mhigo after over twenty years of imperial subjugation. The Resistance under Lyse gathers with the Alliance leadership and, singing the Ala Mhigan anthem, raise their flag.
Following the liberation of their homeland, the Resistance reorganizes into an official army and police force of the newly freed nation, working hard to rebuild their home.Ultima Weapon-based prototypes, the Ruby Weapon. They later assist the Warrior, Gaius, and Garlond Ironworks in liberating the town of Terncliff in southern Werlyt from the Sapphire Weapon.