The chaos comes as Palmero wraps up his time in office. The Liberals and the Traditionalists butt heads over the Church, but the Traditionalists, though somewhat more powerful than the anticlerical Liberals, are themselves fractured into two factions: the Hijos del Pais who advocate for the native priesthood, and the reactionary Ultramontanists who believe the Pope alone has the final say on such matters. The two factions, though united by the maintenance of the Church's sovereignty, struggle and clash on many occasions across the administration of the High Consul.
This comes to a head in 1841 when the Ultramontanists call for the head, or at least the frock, of one Mariano Gomez, a secular priest who has ever fought for the rights of the native priests as opposed to the still largely Peninsular friars.
This protest specifically comes from Fr. Gomez's endorsement of the seemingly heterodox Cofradia de San Jose, a native religious order founded by the lay brother Apolinario de la Cruz, popularly known as Hermano Pule. A boy when the revolution swept through his home province, de la Cruz was deeply influenced by the violence and the chaos he encountered, and at a young age desired to become a priest. Yet he was spurned by the friars of the Dominican order. Undeterred, he worked as a lay brother in the San Juan de Dios hospital, learning public speaking and studying the Bible alongside a brotherhood that allowed natives into their ranks. Eventually, the young man formed his own lay religious order with a secular priest and other comrades in 1832, named the Hermandad de la Archi-Cofradia del Glorioso Señor San Jose y de la Virgen del Rosario (Brotherhood of the Arch-Confraternity of the Glorious Lord Saint Joseph and the Virgin of the Rosary), shortened to the Cofradia de San Jose, or the Confraternity of Saint Joseph. This confraternity was a small association among many, only differing in that it incorporated some folk practices (itself not uncommon) and, because of Brother Apolinario's experience with the Benedictines, it rejected Spaniards both Criollo and Peninsular within its ranks. [1]
The government had remained unaware of this religious order, spending most of its time getting things in order during and after the revolution, but now comes a religious crisis that tears the Traditionalist faction apart. Both sides have certain grievances with the Confraternity, but the Hijos del Pais want merely to bring them gently in line with orthodoxy as Fr. Gomez has convinced them to do, while the Ultramontanists want this blatant heresy suppressed. The judge of this case ultimately rules in favor of the former, but this causes a wound within the Traditionalist faction and allows the Liberals to rise.
The rise of Marcelino Florentino in particular, an anticlerical Liberal from a branch of a prominent Ilocano family, to the position of High Consul begins a series of laws and regulations which strips the religious orders of prime real estate and begins land reform. This would not go uncontested, and Florentino himself would be the target of more than one assassination attempt, but he begins a culture war that will last decades, perhaps even up to the present.
[1] basically OTL, except with a republican government now at the head of the seat instead of Spaniards looking for any sign of dissent, the Confraternity isn't savagely suppressed and instead becomes a point of controversy within the traditionalist faction of the government.