Sequels tend to be more fan service with little or linear story development and here it seems to be the case. Whereas the story continues on throwing in random events, it does little to explain the plot and has left many questions unanswered.
Index is still a fugitive and many powerful Magical organizations and individuals want to take her to use the books in her memory eliminating her in the process. War between those organizations is also starting to emerge. Index can only rely on her friend Touma who has always protected her along with Misaka and other friends from the Academy.
WARNING: MAY CONTAIN SPOILERS.