In Gaul in 52 B.C., two Roman soldiers, Legionary Titus Pullo and Centurion Lucius Vorenus, are tasked with recovering Julius Caesar's personal Eagle, stolen from his camp in the dead of night. With his campaign in Gaul coming to a successful conclusion, Caesar's popularity is continuing to grow. He's saddened however when he receives news from his good friend Pompey Magnus that his daughter, Pompey's wife, has died in childbirth. In the Senate, Pompey must defend the prolonged absence of his friend and co-Consul Caesar against charges of corruption and of waging an illegal war. It's all a ruse however as he is plotting to eliminate him. Meanwhile, Atia of the Julii sends her son Octavian to Gaul deliver a gift of a beautiful stallion to his great uncle Julius Caesar. He is taken prisoner along the way. Fortunately, Vorenus and Pullo rescue him and as a result, both receive Caesar's favor.
With Caesar quickly advancing toward Rome, Pompey begins ordering a retreat and forces his citizens to pick sides. Timon does Atia's dirty work and Vorenus cannot understand why no one is resisting while on a scouting mission.
Atia and her family have stayed behind when Pompey and others fled and she now throws a party for her triumphant uncle, Julius Caesar. She clearly has her sights set on the great leader and is puzzled when he sends her a guest list that includes Servilia of the Junii. She soon finds out why. Pompey wants to find out what happened to the gold from the Roman Treasury and sends his son Quintus to Rome to find out what happened. They go directly to Vorenus' home but he has no idea what they are talking about. Pullo arrives however and Vorenus tells him to go directly to Caesar himself and explain. Octavian meanwhile learns of one of his uncle's secrets.
Caesar contemplates Pompey's counteroffer. Vorenus continues to struggle as a businessman and must reevaluate his career choice. Atia schemes to come between Caesar and Servilia and Pullo seeks Octavian's help.
Caesar pursued Pompey to Greece but the tide has turned and it's Caesar who is on the run. He contacts Mark Antony, who he left in charge in Rome, to come and join him with the 13th Legion but Antony seems to be in no hurry. Vorenus has re-enlisted in Antony's Legion and he and Niobe have begun to renew their marital relationship. The presence of Niobe's sister is the only sour note in their house. Pullo meanwhile continues to train young Octavian in the use of arms and the boy's mother Atia is so pleased with his development that she decides he should take another step to manhood and orders Pullo to take him to a brothel so he can have his first sexual experience. Atia also continues with her scheming ways and believing that Caesar is done for, decides she had better make friends with Servilia.
As they try to reach Caesar in Greece, the shipwrecked Vorenus and Pullo confront an unexpected dilemma. Back in Rome, Atia again sends Octavia to beg protection from Servilia, who complies readily to encourage her growing friendship with Octavia. As they prepare their counterattack against Caesar, Pompey's Republicans begin to squabble over both the anticipated spoils and the method of finishing Caesar off. Niobe's sister Lyde comes back to see her and comforts her over Vorenus's disappearance. Badly outnumbered, Caesar and Antony make their stand at Pharsalus. On his arrival in Egypt, Pompey is greeted by a Roman veteran.
Brutus gets a chilly reception from Servilia when he returns home from Greece. In Egypt, Caesar rebukes the advisers of the boy king, Ptolemy XIII, for their presumption in eliminating Pompey and demands the man who killed him. Caesar decides to intervene in the dispute between Ptolemy and his sister-wife, Cleopatra, to ensure both Rome's grain supply and his own access to Egypt's treasure. Antony, in an unusual show of prudence, advises against this with only half a legion in Alexandria and Cato and Scipio still at large in Africa. Caesar sends Vorenus and Pullo to rescue Cleopatra from house-arrest and escort her to Alexandria. Upon meeting Vorenus and Pullo, the narcissistic, opium-smoking teenage Cleopatra decides that her only hope of survival is to seduce Caesar and she compels Vorenus and Pullo to help smuggle her into the city first by unsuccessfully attempting to seduce Vorenus, but she has better luck with Pullo. Servilia's relationship with Octavia deepens beyond friendship into a passionate lesbian tryst. Caesar is besieged in Alexandra by the Egyptians loyal to Ptolemy. Back in Rome, Antony greets Brutus and Cicero on the floor of the deserted Senate and makes Cicero a promise to kill him if he ever turns against him.
The price of Caesar's mercy: Cicero nominates Caesar to an unprecedented ten-year dictatorship and Brutus speaks in support of the motion. With martial authority and Niobe at his side, Vorenus campaigns for magistrate under Posca's advice, but is shocked to learn from Posca that Caesar has already fixed the election in Vorenus's favor. Meanwhile, Atia continues her humiliation of Servilia while denying any involvement in her assault. But Atia becomes troubled by the silent depression of Octavia after Octavian compels her to return home from the cloister where she had fled. As Servilia lies at home shattered by her recent attack, she soon revives and gets her self-confidence back when she takes in the homeless and embittered Quintus Pompey whom she sees as her tool for revenge against Caeser for leaving her. As Caesar prepares for his Triumph involving five days of celebration and games, Antony finds that the dictator has no sense of humor about the trappings of power. The circulation of a denunciation of Caesar, signed by Brutus, fascinates Rome but stuns Brutus, who suspects his mother. Denied permission to march with the Thirteenth in the Triumph, the dejected Pullo resolves to make a new life as a civilian with Eirene, but his dream leads only to horror for the Vorenii and utter wretchedness for himself.
Picking up exactly where Season One left off on the Ides of March, 44 BC, Caesar has been assassinated, stabbed to death, and his bloody corpse lays in the senate. The rapidly spreading news shocks the city. Even consul Marc Antony must run to the safety of Atia's house where he swears to take bloody revenge on Caesar's murderers, but for the time flees with Caesar's family to the north. But Octavian keeps a cooler head then his mother. Calpurnia insists on the private reading of Caesar's will, which names Gaius Octavian as his adopted son and full heir and makes a gift to each citizen while freeing Posca (the slave who reads it out) with a stipend, but they must fear a rightful tyrannicide will be declared allowing full confiscation. Octavian points out legally declaring Caesar a tyrant would also invalidate all his deeds, including mandates held from him, so Brutus' followers have an interest in a full pardon instead. Hearing about Vorinus accidental killing of Niobe, Pullo rushes to his aid. Meanwhile, Cicero first congratulates Brutus's side, then pays his respects to surprise visitor Marc Antony who presses Octavian's legal logic means elections are necessary, claims Caesar's popular following and offers stability by a deal: Caesar is to be given a state funeral, the republic simply resumes and all terms of office continue. Despite Cicero's suggestion to kill Antony instead, Brutus accepts. Romans massively attend Caesar's funeral pyre; after the speeches, Brutus who was too cerebral is clearly out of popular favor, inspiring retort Marc Antony in. Elsewhere, Vorenus reclaims his children with Pullo, and kills Flavio and his master who admits having raped and killed them.
Lucius Vorenus, the power-hungry "Son of Hades", controls the Aventine but practices a pointless, beastly reign of terror, coming down hard on gang captains for futilities, and nearly ruins his friendship with Pullo, whose efforts to calm things down are mistaken for disrespect and disobedience, even starts a fight once he learns the truth about Niobe; Pullio leaves Rome disgusted. After Atia convinces Marc Antony the governorship of ghastly Macedonia after his consulate would not only be unpleasant but leave him exposed to his dangerous enemies, he puts the heat on senatorial leader Cicero to give him Gaul instead, which once was the base for Julius Caesar's coup d'état. The slave Duro endures male prostitution but most arrogantly demands extra pay and even a kiss from Servilia as it will take more time to commit the planned murder in Atia's home. Marc promises Atia not to hurt Octavian, whose recruiting he calls a joke, after putting down his party's expected plot. Brutus has a hard time controlling himself while soliciting the Bithynian king's financial support to raise an army. Instead of proposing Antony for governor of Gaul, Cicero sends an extremely insulting speech and joins Octavian's growing army.
Servilia's plan to assassinate Atia backfires, with horrific circumstances when Atia's servant Althea accidentally tastes a bowl of poisoned stew before Atia samples it. Atia has Timon and his men abduct Servilia and subject her to hours of physical and degrading torture. But the brutal punishment Atia desires against her mortal enemy is one too many atrocities for Timon, who finally snaps, frees the physically and emotionally broken Servilia, and ends his contentious relationship with Atia at the advice of his brother Levi. In Gaul, with help from the grown-up Octavian, Titus Pullo seeks out Lucius Vorenus on the bloody battlefields where Octavian's armies have nearly wiped out the rebel Marc Antony's legions. Once he finds Vorenus, Pullo sets off with his friend to find and rescue Vorenus' family, sold into slavery. Charged with hand-delivering a message to Octavia, a love-struck Agrippa jumps at the chance to see her again. Meanwhile, Cicero balks at the news that Octavian is returning with his legions to Rome, and leaving the bloodied, but unbeaten, Antony's forces ready to fight another day. In a remote province in Asia Minor, Brutus continues building his own army to retake Rome and destroy both Octavian and Anthony's forces. Working together again as friends and "brothers", Titus and Lucius accomplish their urgent mission with a little intimidation and violence against the slave mine procurator.
Vorenus and Pullo return to the Collegium in Rome with Vorenus' family, but some of the "changes" that Pullo had warned him about regarding his two daughters Vorena both the Elder and Younger, as well as his wife's son, begin to manifest themselves into hostility and resentment. But Vorenus is completely oblivious to this, and is too blissfully happy to return to the role of 'father'. Meanwhile, Octavian finally returns and manages to negotiate the Senate Consul's seat from a scheming Cicero, but in spite of his promise to 'faithfully follow' the older man's counsel, Octavian proves that he certainly has a mind of his own, vowing to hunt down and kill the assassins of Julius Caesar, much to Cicero's consternation. Elsewhere, Brutus and Cassius receive news that might prove useful in staging a triumphant return to Rome, as well as the ultimate defeat of both Mark Antony and Octavian's forces. Also, Atia has a reunion with her son that is strained to say the least, but there is a tentative reconciliation between them. And another, much less stressful reunion between two lovers, Octavia and Agrippa, who saves her from an attempted date-rape at an orgy party, will bring about an unforeseen alliance between two formerly mortal enemies.
Inconsolable at the death of Brutus at Philippi, Servilia makes her final bid to gain the ultimate vengeance against Atia. Meanwhile, Eirene and Gaia have a major falling-out, prompting Eirene to demand that Pullo properly chastise the slave. When he does, the dynamic between the two of them changes in a violent and unexpected fashion. King Herod engages Mark Antony as a reluctant ally by offering a generous gift of 20,000 pounds of gold, and when Posca is excluded from sharing in the windfall, he engineers a move behind-the-scenes that will once again strain the uneasy truce between Octavian and Antony. Vorenus eldest daughter, Vorena, is blackmailed by Mascius into spying on her father after her tryst with one of his men is discovered. The end of two love affairs and a marriage in the house of Julii have major ramifications for life in the city and on the Aventine when Octavian insists on the courtship between Octavia and Mark Antony which irks both Atia and Agrippa. Also, a desperate move to assassinate Herod finishes the relationship between contentious siblings Timon and Levi when they have a falling out, and Levi gets killed by accident.