Two events in particular had played against the reputation of the Society of Jesus in Portugal. Portugal was emerging as a world power. It was punching above its weight on the world scene, in spite of being a small country, it was developing a large seaborne empire in Africa, Asia and South America, specifically Brasil. This brought wealth and power and also tensions with the Jesuit missionaries who were less interested in exploitation and more interested in educating the indigenous peoples. This was to flare up into the War of the Seven Reductions in South America in 1756 , famously portrayed in the Palm D'or winning film the Mission. The war had lain a foundation of anti - Jesuit propaganda in the court of Lisbon. Pombal and others were outraged at the Jesuits involvement in the lucrative work of the 'reducciones' and defence of the indigenous Guarani Indians. The Jesuits were seen as getting in the way of the economic plunder which Portugal so desired.
Secondly there was the famous Lisbon Earthquake in in 1755. The emerging world city of Lisbon was destroyed and many killed in the tsunami that followed. Strikingly the earthquake struck on All Saints Day, at 9.40 in the morning - when many were in church. It was the churchgoers who were more likely to be killed by falling buildings and the fires that ensued. It coincided with a time when the Enlightenment was growing in influence, with its attendant anti-religious sentiments as it emerged from the Medieval world. The secularising pressures grew due to the unfortunate timing of this disaster, as many entered a crisis in faith.
Pombal efficiently and impressively coordinating the rebuilding of Lisbon and grew in stature and power due to this. The famous Jesuit Malagrida preached and published that the calamity of the Earthquake was the punishment of a just God on a sinful people. Reminiscent of modern fundamentalist and obscurantist preachers - this backfired on the Jesuits reputation, and handed their enemies a propaganda coup. Pombal resented the implicit criticism of the government. Malagrida was to be executed in a barbarous manner within 5 years with the Society exiled from Portugal. Ironically by doing so - Pombal the great champion of the 'enlightenment' was to dismantle the most effective and prestigious education system in the Portugese world - 20 colleges in Portugal and 30 in their colonies. It was a strange act of self mutilation, particularly at a time when both England and Holland had eclipsed Portugese influence and power.