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She was referring to a war between the Silence and the Doctor, however it is unknown if we have actually seen any of this war yet, or if the events of past episodes such as the TARDIS explosion were part of this so-called war. Either way, the reaction from the Doctor in "A Good Man Goes to War" suggests that it was the first time he had heard that he was part of this war, yet that doesn't mean that the war had already been raging against him without his knowledge.

She was referring to the Seige of Trenzalore, which where the Doctor would die without revealing his true name to free the Time Lords. As a result of the fear that this possibility presented all of the Doctor's enemies converged on Trenzalore with the intention of killing him to prevent the Time Lords' return. The most vile were the Daleks, who ended up attacking the Papel Mainframe and converting the populace into Dalek Puppets. What remained of the Confessional Priests, which were genetically engineered to make people forget things (and thus are the monsters that tried killing him; however, the previous ones were from a rogue faction ), joined forces with the Doctor to defend Trenzalore for over a millenium - 1000 years.