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The New Dalek Empire was a recreation of the old Dalek Empire, which was destroyed during the Last Great Time War.
First attempts
The New Dalek Empire was to be the new Empire of the Daleks that the Cult of Skaro had planned to create. Time traveling from London in 2007 to New York City in 1930, the Cult, now the last four Daleks in existence, attempted to conquer Earth and recreate the Dalek Empire.
This attempt, even with the help of the Final Experiment (which included use of Pig Slaves and Human-Dalek hybrids) failed due to the interference of the Doctor. At the end, Dalek Caan was the last surviving Dalek. (DW: Daleks in Manhattan / Evolution of the Daleks)
New Empire
Caan activated an emergency temporal shift to escape the Doctor, and ended up at the Gate of Elysium during the Last Great Time War. Travelling into a time-locked era ruined his mind, but he helped to save Davros from his death. Davros, like the Dalek Emperor who also surivived the Time War by time travel, rebuilt the Dalek Fleet of two thousand ships and millions of Daleks - unlike the Emperor, Davros rebuilt the Daleks out of his own Kaled cells. Caan was left as a sort of prophet, and a new Dalek Supreme was created to oversee the Dalek forces.
The Daleks moved 27 planets into the Medusa Cascade from various times and places (mostly mid-2009, but from other eras as well). These made a large device when put together. The new Daleks then took control over the planets in the Cascade, apparently concentrating their forces on Earth. They took many Humans on board their ships, and wiped out any resistance. (DW: The Stolen Earth / Journey's End)