Method of operation
Its main weapon was a beam that pushed objects out of the spacetime continuum, effectively erasing them from history. Careful and meticulous calculations were required to create the exact changes in the timeline that were desired. The ship could be deployed against an entire species by firing the weapon on the species' homeworld, pushing the species out of the spacetime continuum. This caused a causality paradox; all of history the species played any part in would be altered.
The following gallery is an illustration of the method of operation, in which the weapon was used against a colony.
Capabilities and limitations
The ship obtained its power to affect time from its temporal core. When in operation, the core also kept the ship, and everything and everyone on it, outside of normal space-time. This rendered the ship immune to all conventional weapons and protected the crew from the flow of time, effectively rendering them immortal. Perhaps because of this, the ship's conventional defenses were rather limited. Furthermore, the vessel's great mass prevented it from exceeding warp 6. (VOY: "Year of Hell", "Year of Hell, Part II")
The first use of this weapon ship was in a temporal incursion against the Rilnar. The Rilnar had removed the Krenim Imperium as the dominant power in that region of space. Thus an alternate timeline was created in which the Krenim Imperium remained the dominant power. However, there was an unfortunate side effect, unexpected by Annorax: the Rilnar had introduced a vital antibody against a certain disease into the Krenim physiology. The erasure of the Rilnar also therefore erased the antibody, and without it, fifty million Krenim died of the disease. Annorax therefore attempted to undo the erasure with another incursion. But this incursion caused him extreme personal loss: the Krenim colony at Kyana Prime was erased, and with it, his beloved wife.
The weapon ship remained in operation for the next 200 years as Annorax, obsessed with restoring the Kyana Prime colony, and with it, his wife, altered history repeatedly, causing one causality paradox after another. Known species it was used against were the Zahl, the Garenor, the Ram Izad, the Malkoth, and the Alsuran.
Use against Voyager
The weapon ship was also employed against the Federation starship USS Voyager (Component 049 Beta in their calculations). Voyager had been passing through what in a previous timeline had been Zahl space when Annorax used the weapon to erase the Zahl, turning Zahl space into Krenim space. Attacked repeatedly by Krenim warships using chroniton torpedoes against which their deflector shields were useless, they were forced to develop temporal shields to use against the torpedoes. These shields disrupted the precise calculations Annorax' crew had made to direct the results of their temporal incursion against the Garenor. This caused the incursion to "miss"; instead of the desired results, that is, the restoration of all of Krenim territory, including Kyana Prime, a timeline was created in which the Krenim Imperium never existed at all. This was, of course, totally unacceptable, and thus Annorax turned the weapon on Voyager. Voyager, however, was able to escape by going to warp speed, taking advantage of its faster warp capability to outrun the weapon ship.
The weapon ship itself was eventually erased from history when Voyager, all but destroyed by Krenim attacks, led a small fleet, composed of two Mawasi cruisers and three Nihydron warships, against it. Tired of the seemingly endless and futile mission, some of the crew, led by Annorax' second in command, Obrist, shut down the temporal core. This caused the ship to phase back into normal space time, so that conventional weapons could affect it. Though the vessel's conventional weapons were limited, they were still enough to overpower the attackers.
However, Voyager's captain, Kathryn Janeway, was aware of the exact location of the ship's temporal core. Alone on her ship after being forced to order the rest of her crew to abandon ship due to its ruined state, she piloted it into that section in a kamikaze attack, causing the core to destabilize. This exploded the weapon ship and, moreover, caused a temporal incursion that erased the ship itself from history, and with it, every one of the alterations in the timeline it had ever made.
Ironically, this had the effect of accomplishing exactly that which Annorax had been attempting to do; Kyana Prime was never erased, and Annorax never lost his wife. (VOY: "Year of Hell", "Year of Hell, Part II")