Evacuation of Skaro

Following the alterations to the timeline created when the Tenth Doctor poisoned the Kotturuh during the Dark Times, (PROSE: The Guide to the Dark Times, The Knight, The Fool and The Dead) the evacuation of Skaro was the result of a failed Dalek attempt to defend their homeworld of Skaro during an attack from the Entity, a mysterious time sensitive opponent that sought to control N-Space.

The Entity had been unleashed by the Archivians to force the Daleks of the Restoration Empire off Islos after they invaded. Using its existence outside of time to its advantage, the Entity arrived at Skaro before the Dalek Fleet escaping Islos could and attacked the Dalek City. Though, as suggested by the Executioner, all Daleks on Skaro launched an assault against their new foe, their firepower was insufficient. The Emperor then ordered a planetary evacuation. However, the Entity destroyed the escaping Daleks and their flying saucers. (WC: The Sentinel of the Fifth Galaxy)

Aftermath
With their escape attempt foiled and Skaro lost to their enemy, the Emperor and his fleet were left without reinforcements, so the Dalek Prime Strategist travelled to the Fifth Galaxy to awaken a hidden Dalek army. However, the Entity corrupted the base's Sentinel, which proceeded to corrupt the army. The army was destroyed with the barren planet by the Dalek Flagship, so the Emperor's forces were again left without aid, but the Entity was weakened. (WC: The Sentinel of the Fifth Galaxy)

After making it seem like the Restoration Empire had been brought to its knees, (WC: Day of Reckoning) the Emperor and Strategist allied with the Mechonoids to defeat the Entity in the Battle of Mechanus. Many Mechanoids were killed in the battle, and the Mechanoid Queen vowed to destroy the two Dalek units, who she believed to be the last Daleks in existence. (WC: The Deadly Ally) In reality, a number of Daleks remained hidden in the ancient underground bunkers on Skaro, and more Daleks had been away from the Emperor, theorized by Mechanoid 2150 to be Daleks that had evacuated Skaro. Nevertheless, when he and Prime Strategist arrived on Skaro, the Emperor proclaimed that they had reclaimed the planet and recalled the Daleks there. When the Mechanoid Queen and her forces arrived to destroy the Dalek City on Skaro, they were confronted by the army of Dalek survivors. (WC: Day of Reckoning)