The second season of Toaru Majutsu no Index is for the most part a build-up for an ongoing story. Season two ends abruptly so there is little doubt another season is planned. Whether it gets made is another matter.
Season two focuses on Kamijou Touma's encounters with the Catholic Church, which is not portrayed in a flattering way. To put it bluntly, they are a bunch of anti-science lunatics and thugs. Other Churches in the series, such as the Church of England, are moderate by comparison, although not above devious acts. In case you think this is a statement against religion, the leaders of Academy City, the supposed centre of scientific study, are no paragons of virtue either, as they are clearly manipulating Touma.
Touma, whose bad luck always puts him in the wrong place anyway, upsets a number of the Catholic Church's dastardly plans. Seeking revenge, the Church accelerates its plans against Academy City itself which is the natural enemy of the science hating Catholic Church. The Church launches two attacks which are both thwarted, but such openly hostile action is effectively a declaration of war between the Catholic Church and Academy City.
And just as it starts to get really interesting, that, annoyingly, is where season two ends! It's a great set up for the action to come; hopefully the story will be continued.