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In the timeline created (PROSE: The Guide to the Dark Times) when the Tenth Doctor poisoned the Kotturuh during the Dark Times, (PROSE: The Knight, The Fool and The Dead) the evacuation of Skaro was a failed Dalek attempt to defend and then evacuate their homeworld of Skaro from the 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 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)
By the time they were in the midst of a losing war against the Hond, (COMIC: Defender of the Daleks) a race that had also been unleashed by the invasion of Islos, (PROSE: The Restoration Empire) the Daleks had taken back Skaro. Additionally, when the Tenth Doctor was brought to the Restoration Empire during this war, the Daleks made no mention of the Entity. (COMIC: Defender of the Daleks)