Protoforms are part of the Cybertronian's life cycle. Normally they are given life by the Well of Allsparks; once they are brought to life, they are required to scan a vehicle that would be natural for the caste they were placed in (though the Covenant of Primus implies that they are born with certain altmodes).
In their long deep space travel, Cybertronians may revert to their protoform state in order to conserve energy in stasis. This can help with conserving energy and body through space travels.
Five protoforms were stored in a laboratory aboard the Harbinger. When Starscream found them, he turned them into clones of himself. These clones, linked to Starscream's very spark and will, were sent on a mission to assassinate Megatron. Of the five, only one escaped, and was later killed by Starscream himself when it attempted to terminate him.