On routine patrol, the Enterprise happens upon space debris from the S.S. Beagle, a survey ship which disappeared 6 years ago. The Beagle had been a Class 4 star drive vessel with a crew of 47, and had been commanded by Captain R.M. Merrik, an academy associate of Kirk. When Spock projects the path of the wreckage back in time, he discovers a civilization of modern-day Romans on Planet 4 of the 892 System. The Enterprise then intercepts a television transmission showing a gladiator killing the ``last of the Barbarians,'' who turns out to be Beagle flight officer William B. Harrison.
After beaming down, Spock, Bones, and Kirk are confronted by a cadre of rifle-toting escaped slaves. The landing party is captured and taken to the slaves' leader Septimus, a former Senator who now worships the ``sun.'' Although the slave Flavius wants to kill the Enterprise's landing party, Septimus accepts them as friends and offers them hospitality. The extreme similarity of the 892 System's civilization to the Romans Earth is apparently a coincidence, demonstrating according to Kirk the validity of Hodgekin's Law of Parallel Planet Development.
When Kirk questions the slaves about a man named Merrik, he finds that the leader and First Citizen of the Roman-like empire is called Merricus. When Kirk and his comrades then express an interest in capturing Merricus, Flavius Maximus (a former gladiator) offers to accompany them. However, they are captured by Roman forces and put in prison. Kirk questions Flavius to find out about the institution of slavery on this planet, and finds that slave uprisings virtually ceased after they were slowly given rights such as medical care and a pension. Kirk, McCoy, and Spock attempt to escape when their guards escort them to talk to Merrik, but Merrik has anticipated this, disarms them, and then brings them to his quarters for a conversation.
Merricus is indeed Merrick, and he tells Kirk that he beamed down to the planet to obtain iridium ore for repairs after he Beagle sustained meteor damage. Here, he met First Consul Claudius Marcus. He also decided that he could not bring word of the planet's culture to the Federation without hopelessly contaminating it. Merrik therefore agreed to stay, but killed those of his crew members who could not adapt by sending them into the Arena be killed in a fight. The Consul orders Kirk to transport his crew down a few at a time. Instead, Kirk gives the code word ``condition green'' alerting Scott that he is in trouble, but that Scott should not interfere. For refusing to comply, Merrik sends McCoy and Spock to fight in the Arena against gladiators Achilles and the recaptured Flavius. Spock is very unsporting, however, since he stuns his opponent and then nerve pinches Flavius when McCoy gets into trouble. McCoy and Spock are returned to prison, but Kirk is entertained by the Proconsul's slave Drusilla prior to execution.
Scott prepares to disrupt power to the entire planet from the Enterprise just as Kirk is about to be executed on live Roman TV. Before the execution can take place, Flavius intervenes. Unfortunately, he is killed by machine gun fire before Scott cuts power. Kirk then frees McCoy and Spock, only to be surrounded by Roman guards. However, Merrik has stolen a communicator and signals the Enterprise to beam them up. Unfortunately, in the middle of his transmission, he is slain by the Proconsul. Merrik throws the communicator to Kirk, who has Scotty beam them up just before their cell is criss-crossed with machine gun fire. Back aboard the Enterprise, Uhura discovers that the escaped slaves were not sun worshippers, but worshippers of a different ``son'': the Son of God.