A Nether Rift was a "gateway" between Ratchet's universe and the Netherverse. These unnatural rifts were formed eons ago by explosion of the Great Clock as the result of the fongoids misuse of time travel that had been given to them by the Zoni. These rifts allowed some nethers to enter a parallel universe in limited numbers. Mr. Eye used such rifts to talk to Vendra Prog, whom was staying at the Meero Orphanage on planet Yerek.
After Pollyx upgraded Clank with a Rift Cracker (a device that allowed Robots to enter and exit a reality), Clank was able to find such rifts and enter the Netherverse.