The Twilight Annihilator is a weapon that was created during the Dark Times of the Universe, made to completly destroy galaxies using technology that could create both a supermassive black hole and a 'supermassive white hole', which consumes the target and cancels out the black hole to avoid unneeded destruction.
The exact creation of the Twilight Annihilator is unknown. However, it is thought that the Gandrians, Ha'ahl or even the Time Lords created it as they had quite advanced technology during the turbulent Dark Times.
Use and Banning
Upon the eve of the Dark Times, Twilight Annihilators were used far more often and the Universe's expansion was affected becasue of it. New life and hospitable places were exterminated before they could fully develop or develop at all, because of the countless wars being waged - most of them sparked from use of the Annihilators.
The newly-established Shadow Proclomation banned the use of the Twilight Annihilators and punished any further use or even the threat of use would be punishable by disintegration. Blueprints and instructions on their creation were also destroyed, yet many believe that some records survived.
The Annihilators were created using several 'super black hole' converting devices amidst a gigantic hadron collider. The more converters within the device, the bigger the overall black hole and scale of destruction. Fear of overstepping boundaries with the devices have led to them being to powerful to use or to be created with only the maximum ever to be 13 converters - enough to obliterate several clusters of galaxies.
The converters are detonated via remote activation and instantly create the giant black hole, devouring all mass, light, time and space into it. The collider stays out of the massive gravitational pull by slowly bleeding out the white hole's energy to keep itself pushing away from the black hole. After the converters are all detonated, the collider automatically activates and consumes the black hole, and fading away because of the damage done to it. It leaves no trace, only a blank space of vacuum where the galaxies once were.
An Annihilator is activated when the remote is used to operate the mechanism that holds missing peices of the Annihilator, waiting to be put in place and destroy its target.
How to dispose of an Annihilator
An Annihilator is unable to be of use without the remote. The remote is the only way to have the mechanism put the inactive peices in place. Without it, the Annihilator is useless and can be destroyed without fear of creating the black hole. For complete certainty that it is no longer a threat, the Annihilator must be vapourised via thermonuclear radiation (like being pushed into a star).
The Ninety-Nine was the largest, and therefore most dangerous and powerful Twilight Annihilator in creation. The name alludes to the number of converting devices, which held 99 of them. If 13 devices can destroy a large number of galaxies, 99 would obliterate half of the entire universe. It was created by the Master, in hopes of exterminating what he saw as the two 'most dangerous races in existence' - the Daleks and the newly resurrected Time Lords.
The Master's nihilistic hatred for both himself and his species, coupled with the inherent loathing of Daleks in all Time Lords, compelled him to devise a way to destroy both of them. Also, he planned to destroy his old enemy, the Doctor, because it was his DNA and TARDIS which assisted in recreating New Gallifrey and restoring the Time Lords. The Master would allow himself to die as well, as he was both something he despised and knew that the despair within him after destroying so much and having no other goal to live for would eat away at him and force him to discontinue his existence.
The Doctor foiled his plan but the Master still attempted to dispose of the Doctor, himself and the Daleks. After damaging the reactor of the Dalek mothership (which also linked to every other ship), and making it go critical so he would destroy them all. The Doctor escaped in the TARDIS, leaving the Daleks and the Master to die. The reactor contained enough thermonuclear raadiation to dispose of the inactive Annihilator (the remote was blown apart by a stray Dalek energy beam).