The Restoration Empire was, according to one source, (PROSE: The Restoration Empire) the incarnation of the Dalek Empire which rose from the ashes of the Imperial Dalek faction following the close of the Imperial-Renegade Dalek Civil War.
Although the Restoration Empire appeared to be a natural part of the Dalek race's history, the Empire's Dalek Scientists would go on to discover evidence that the Restoration Empire only came into existence as a result of the divergences in time (PROSE: The Restoration Empire) caused by the Tenth Doctor rendering the Kotturuh extinct in the Dark Times. (PROSE: The Knight, The Fool and The Dead, All Flesh is Grass) The Time Lords, in a compendium of Dalek history, likewise listed the Restoration Empire, specifically its Time Squad, among the many Dalek anomalies that they could not readily place along their foes' timeline. (PROSE: Dalek Combat Training Manual)
Either way, the earliest definitive foundations of the Restoration Empire occurred during the Imperial-Renegade Dalek Civil War, where a Dalek Supreme who would later become the new Dalek Emperor served on the Dalek Council of the Imperial Daleks. After Davros fled the war, the Supreme exterminated all other members of the Council (PROSE: The Restoration Empire) and was elected the new Emperor of the Imperial Daleks. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe) Modelling himself on a former ruler, he built himself a gold casing which augmented his brain capacity, becoming the Emperor of the Restoration.
From this position, the Emperor sought to restore the Dalek Empire to its former glory through a new hierarchy of Dalek command and a new system of production. He restored Skaro and overhauled the standard Dalek hierarchy, bringing back Silver Daleks as drones. (PROSE: The Restoration Empire) Also among the Emperor's forces was the Dalek Prime Strategist, a unit who claimed to be older than the Emperor. (COMIC: Defender of the Daleks)
Human historians believed the new Emperor carried out Davros' plan of moving against the High Council of the Time Lords, instigating the Last Great Time War. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)
Shift in the timelines
An altered history
When the Tenth Doctor poisoned the Kotturuh in the Dark Times, (PROSE: The Knight, The Fool and The Dead) he caused fluctuations in time, (PROSE: The Guide to the Dark Times) resulting in the Restoration Empire not appearing to fight the Last Great Time War. (COMIC: Defender of the Daleks)
The Emperor received a message from an ancient Dalek drone, and he realized the unit was a survivor of a Time Squad that had yet to be sent back in time. From the message, the Emperor concluded that history was under attack, which the Dalek Empire was vulnerable to, and that the Doctor was involved, but still needed more information. Deciding the required information could be found somewhere like the Archive of Islos, (PROSE: The Last Message) the Emperor personally led a Dalek fleet to Islos to take the contents of the Archive.
Though the Dalek force overcame all resistance, the Chief Archivian made a deal for the rescue of the Archive with the Entity, promising it the Daleks. When the Emperor and his Daleks, including the Strategist and Executioner entered the Archive, they realised it was empty. The Chief Archivian informed them of its deal as the Entity emerged from a portal. (WC: The Archive of Islos) The Daleks retreated from Islos and returned to Skaro, pursued by the Entity. It attacked Skaro and the Daleks' firepower proved ineffective, forcing the Emperor to order an evacuation. The Strategist advised that the evacuation was failing and they should abandon the planet. The realisation that Skaro had been lost caused the Emperor to fall silent, forcing the Strategist to coordinate the retreat. After the Strategist suggested reinforcements, the Emperor decreed that the Sentinel of the Fifth Galaxy was required. The Strategist was sent to meet the Sentinel and awaken a dormant army of ten-hundred Daleks, but the Entity compromised the army and took it over. As the Executioner led Dalek forces against the army, the Strategist advised the Emperor to withdraw again as they could not sustain further losses and defended its failure. (WC: The Sentinel of the Fifth Galaxy)
The Strategist put together a scheme to destroy both the Entity and the Mechanoid Empire. (WC: Day of Reckoning) The Emperor and Strategist travelled to Mechanus and claimed to seek the Mechonoids' assistance in defeating the Entity, though in truth they were deliberately luring the Entity there. Noticing his small group of Silver Dalek guards not being reinforced after being destroyed by Mechanoids, the Mechanoid Queen wondered if the Emperor and Strategist were the only two Daleks left. (WC: Planet of the Mechanoids) In reality, the rest of the Daleks were alive, and this was another phase of the Strategist's plan. It wanted the Mechanoids and the rest of N-Space to believe the Daleks had been devastated by the Entity to lure the rival empire into a false sense of security. (WC: Day of Reckoning) Shortly after the power of the Mechonoid City was drained and the Emperor revealed to the Queen that he had lured the Entity there. (WC: Planet of the Mechanoids) A number of Mechanoids were destroyed in the ensuing battle against the Entity, and the Emperor himself fought it. Using the orbital defence grid as a beam projector, the Strategist and Mechanoid 2150 banished the Entity back to its own reality. Angered at the Daleks bringing the Entity to them, the Mechanoid Queen, under the impression that they were the last of the Dalek species, then ordered the Emperor and Strategist to leave Mechanus and vowed to destroy them. (WC: The Deadly Ally)
The Emperor and Strategist returned to Skaro and reactivated the Dalek City. The Emperor then recalled his forces to Skaro, and, when the Mechanoid Queen and her forces arrived, they were caught off guard by Dalek drones, beginning a fierce battle. As the Mechanoid army was overwhelmed, 2150 speculated the Dalek reinforcements had been hiding in ancient bunkers or were units that had successfully evacuated Skaro. Nevertheless, the Queen, 2150, and several others entered the control center and attempted to turn the Strategist against the Emperor. It appeared to agree, making the Emperor believe the Strategist was a traitor, and the Strategist brought 2150 to a beam projector chamber. After allowing the Mechanoid to update the technology under the pretense that it would be used to send the Emperor away to the Entity's dimension, the Strategist took control of the weapon, claiming it needed to send Daleks that would not be loyal to its rule through the portal as well. In reality, however, the Strategist then used the beam projector to send the entire Mechanoid army through the portal, securing a Dalek victory. The Emperor then praised the Strategist's plan, citing that both the Entity and the Mechanoids, which it claimed to be the two greatest threats to the Dalek Empire, were now defeated. However, the Entity then managed to take over a ruined Mechanoid, taunting the two Daleks by revealing another threat was coming. (WC: Day of Reckoning)
Accordingly, the Daleks were attacked by the Hond, (COMIC: Defender of the Daleks) having been unleashed by the invasion of the Archive of Islos. (PROSE: The Restoration Empire) With Skaro in danger of falling to the Hond, the Prime Strategist suggested the Doctor be used against the Hond. The Tenth Doctor was captured by the Daleks and brought before the Emperor. He recognised the Empire he was interacting with, who had never fought in the Last Great Time War, as "a paradox". The Emperor convinced him to help them and sent him to meet the Strategist. Together, they investigated the Vault of Obscenities and discovered a way to pacify the Hond, deploying it just as the Hond reached Skaro's defences. The Daleks turned on the Doctor, but he escaped with the aid of the Thirteenth Doctor. The Strategist met the furious Emperor, defending its failure, and suggested the Daleks could use the Eighth Doctor. (COMIC: Defender of the Daleks)
Journeys in the Dark Times
Eventually the Emperor sent a Time Squad to rectify the temporal fluctuations to the Dalek Empire's benefit. (PROSE: The Guide to the Dark Times) Having discovered the source of the fluctuations to be in the Dark Times, where their own timeships could not travel, the Time Squad planned to recruit the Eighth Doctor to help them, intending to use his TARDIS in order to travel back there. (PROSE: The Restoration Empire) The Emperor also recorded orders for the event of them failing to restore the proper timeline. (PROSE: Mission to the Known, All Flesh is Grass)
The Squad captured the Eighth Doctor by pulling his TARDIS away from Atharna, (AUDIO: He Kills Me, He Kills Me Not) and recruited him to help their investigation. They travelled together to Wrax, nominally to study its alleged timeline, but also to pursue the Daleks' interest in their superweapon, the Devolver. Whilst the Strategist and the Doctor investigated the Wraxians' gallery, the Time Commander, Scientist and Executioner met the Wraxian President, who agreed to demonstrate the Devolver and consider an alliance with the Daleks. She betrayed them and prepared to use the Devolver against the Daleks, prompting the Commander to order the Squad's Drones to invade Wrax. The Doctor negotiated a settlement with the President for the Devolver's dismantling in return for the Daleks' withdrawal, which the Daleks accepted at the Strategist's urging, but the Commander secretly sent the Executioner back to wipe out the Wraxians with the Devolver.
The Doctor revealed he had discovered the source of the alterations on Wrax and devised, seemingly on his own, the plan to use his TARDIS to help the Dalek timeship travel back to the Dark Times. As a result, the Strategist deemed him successfully manipulated. (AUDIO: The Enemy of My Enemy) In the Dark Times, the Daleks, led by the Eighth Doctor, traced the source of the alterations to Mordeela (PROSE: All Flesh is Grass) and confronted the Tenth Doctor's mercenary fleet alongside Vampires allied with the Ninth Doctor. (PROSE: The Knight, The Fool and The Dead) In the ensuing Battle of Mordeela, the Daleks and Vampires destroyed all of the fleet save the flagship, but were unable to prevent the destruction of Mordeela and the Tenth Doctor escaping. (PROSE: All Flesh is Grass)
Believing they had failed to restore the timelines, the Daleks enacted a contingency plan to capitalise on the situation by experimenting on unique lifeforms of the Dark Times. (PROSE: Mission to the Known) The Commander also dispatched Scout Ships to wipe out the last of the Kotturuh, fearing their judgement on the Daleks. (PROSE: All Flesh is Grass) The Time Squad harvested the population of Velosia, under the pretense of saving their best citizens from the Kotturuh. (COMIC: Tales of the Dark Times) The Eighth Doctor found himself sidelined, as he was only needed to ensure they could escape the Dark Times, but was allowed to join their explorations, (PROSE: All Flesh is Grass) including an abandoned spaceship with a source of Huon energy. (COMIC: Tales of the Dark Times) Seeking a Vampire for the Symbiont experiments, the Daleks attacked the Ninth Doctor's coffin ship. ninth incarnation in his TARDIS. (PROSE: All Flesh is Grass) After he left, the Commander and Executioner received pre-recorded orders from the Emperor ordering them to destroy Gallifrey to prevent the rise of the Time Lords. (PROSE: Mission to the Known) The Strategist and Scientist, not privy to these new orders, continued to experiment on the unique lifeforms of the Dark Times, aiming to create a more biologically efficient form of Dalek - the Symbiont.
A Dalek Scout Ship followed one Vampire, Ikalla, to Entranxis, where she was being held by the Death Brokers. The three Doctors were also on Entranxis and helped her escape. The Daleks destroyed an oncoming Kotturuh ship and then set Entranxis' atmosphere alight as their target was lost. The Daleks subsequently found a coffin ship transporting a Great Vampire and captured it. As the Eighth and Tenth Doctors infiltrated the Dalek saucer with Brian the Ood and a Bloodsman, the Scientist extracted the Great Vampire's DNA and infused it into a Dalek mutant to create the Symbiont, an undead Dalek. This caused a significant power drain, leading to conflict between the Commander and Strategist, which enabled the Doctors to escape and Brian to hide. Brian saved himself from the Daleks by wiping himself to an explosive in the engine room and informed the Doctors of the Daleks' destination - Gallifrey. The Doctors rescued Brian and mounted a defence of Gallifrey, facing an army of Dalek Drones enhanced with the Symbiont DNA that the Strategist had created to counter their defense. The original Symbiont was sent to Birinji to kill Inyit, the last of the Kotturuh, but she killed it by judging it. This judgement also wiped out the enhanced Drones, throwing the Daleks into a panic, as they feared the judgement spreading to pure Dalek DNA, and ending their assault, despite the Strategist's demands to press the attack. The Eighth Doctor boarded the saucer and detonated Brian's explosive, forcing the ship into the Time Vortex. (PROSE: All Flesh is Grass)
The Eighth Doctor continued to sabotage the ship, leading to it beginning to break apart in the Vortex. The Strategist attempted to bargain with him to escape in his TARDIS, but the Doctor exposed the deal to the Commander, leading to a firefight between the two. The Strategist killed the Commander, prompting the Drones to turn on him as a traitor which enabled the Doctor to escape. (AUDIO: Mutually Assured Destruction) As the ship collapsed, the Daleks were torn apart by the time winds, (PROSE: Exit Strategy) though one Drone survived, ending up adrift in space. (PROSE: The Last Message) It was eventually brought onboard the Starship Future, where it rebuilt its casing and sought to create a new army from the dormant passengers. It encountered the Fourth Doctor, who believed it defeated, but it had managed to survive again. (AUDIO: Genetics of the Daleks)
Back into the Time War
The Prime Strategist survived, using Kotturuh crystals he had stored in his casings to escape the Vortex by powering an emergency temporal shift. As he fell, he mused that all signs pointed to the Dalek Empire one day waging a war against the Time Lords, and pondered usurping the Emperor to lead the Daleks through it. (PROSE: Exit Strategy) Thus, the Time War was restored to history. (TV: The End of Time, et. al)