Perhaps in between the events of Crash Bandicoot: Warped and The Wrath of Cortex, Coco had been working on this machine. Coco finished the final adjustments on the device when she was interrogated by Aku Aku on the development of the machine, and thus the game's story began there.
As soon as Crash and the crew enter the VR Hub for the first time, Doctor Neo Cortex tells Crash of his plans for world domination, this time having nothing to do with the Crystals as they are a detriment to his plans. He unveils how he's going to control the world: with Crunch, his second bandicoot creation. The message ends after Cortex says that he made a mistake with Crash.
The VR Hub's primary function is to carry Crash to where a Power Crystal is located, via special travel, within the hub that Crash is in, which excludes the secret hub. Crash must find the 5 Crystals within that hub before the portal to the boss fight of that world is unsealed, allowing him to once again return the Elementals back into the state of hibernation they were in before being reawakened by Uka Uka.
When Crash imprisons a mask, he will gain a Super Power in the process (there is one exception to this rule, as it is located in a normal level: Banzai Bonsai). Eventually, all of the hubs lead up to Cortex himself.
Regardless of the level that Crash selected to be his first in a hub, (like choosing Tornado Alley rather than Arctic Antics for Stage 1.) he will encounter the Elemental for that hub for the first time, i.e. Rok-Ko to Earth, Wa-Wa to Water, etc., trying to intimidate Crash into not collecting the Crystals which undoubtedly fail to deter the marsupial. They will also occasionally pop up when Crash re-enters a level for a Relic or missed Gem until he defeats Crunch and said Elemental in a boss fight. However, in the space hub, it is Dr. Cortex who appears instead, and in the secret hub, there are no cutscenes as there is no boss of the hub.