The Dark Time is a term used by Matoran to refer to the thousand year period between the Great Rescue and the coming of the Toa Mata.
During this period the Matoran of Mata Nui were harassed by Teridax using Rahi and the Matoran of Voya Nui struggled greatly without Turaga Jovan. Mahri Nui also broke off from Voya Nui during this time and landed in The Pit. Matoran elsewhere in the universe struggled too, especially on the Tren Krom Peninsula where the Matoran were harassed by Icarax and an army of Manas.