MetaBits are the prestige currency of the game and are used to improve the Reality Engine the simulation runs on. They are earned by "Rebooting", which first becomes available after buying a single Singularity. Afterward, a Reboot can be initiated at any time. You gain MetaBits by increasing the total amount of Ideas and Entropy in a single universe.
The total amount of MetaBits earned is the "simulation level," which passively increases the production multiplier by itself. This is independent of the amount of MetaBits on hand, which can be spent in the Reality Engine tree to increase production, click value, or offline production value.