(covers information from several alternate timelines)
Chroniton torpedoes were ship-mounted weapons utilized by the the Krenim, a Delta Quadrant species which possessed deadly weapons based on temporal science. The torpedoes were capable of passing directly through an enemy's shields due to the fact that they were in a constant state of temporal flux.
In an alternate 2374, the USS Voyager found themselves under near-constant attack by the territorial Krenim, who utilized chroniton torpedoes to inflict severe damage. Eventually, the crew developed a plan to remodulate their targeting scanners to a parametric frequency, so that they could destroy the Krenim's torpedo launchers before they fired. The plan worked, but not before a chroniton torpedo fragment became lodged in Voyager's hull, leaking chroniton radiation into the ship, necessitating inoculations for the entire crew. Five years later, the dormant chronitons in Kes's cells would be reactivated by exposure to a biotemporal field, causing her to experience a series of backward time jumps. These time jumps were halted in 2373, when The Doctor exposed Kes to a precisely modulated field of antichronitons to purge her system of the radiation. (VOY: "Before and After")
In another version of this timeline, Lieutenant Commander Tuvok and Seven of Nine were able to develop temporal shielding which effectively protected Voyager from the Krenim's chroniton torpedoes. This was accomplished by matching Voyager's shields to the temporal variance of the torpedoes, and matching the deflector array to the inverse of that variance. This timeline later negated when the Krenim weapon ship was erased from history, reversing all of the damage it had caused to the timeline from history. (VOY: "Year of Hell", "Year of Hell, Part II")
In the novel A Pocket Full of Lies, Chakotay learns that the temporal anomaly that caused Voyager to be fractured across multiple time periods ("Shattered") was actually the result of a chroniton torpedo fired at Voyager by the Krenim in an attempt to prevent Voyager from disrupting their new peace after Janeway's actions undid Annorax's temporal manipulations. While their plan to regress Voyager back to a point before their involvement in the conflict failed, they were able to take a past, alternate version of Janeway prisoner, resulting in her becoming a leader in a protracted conflict on a disputed planet between the Zahl and the Rilnar with the goal of preventing her from taking any action to disrupt the Krenim Imperium.