Plagued with guilt over the arrest of fellow playwright Baxter, whom Marlowe set up, Will confesses to Alice about his family ties to Catholic priest Father Robert Southwell. Later, the theatre's future is threatened when a rival playhouse, The Rose, offers the crowd-pleasing actor Kemp a better role, forcing Will to offer to write a play just for him.

After writing a dull script, Will is thrown out of Burbage's theatre and left penniless. However, he has an epiphany that there are hidden patterns in successful plays which could give him inspiration. Alice helps him write a better play by stealing the plot from a Spanish book. The Two Gentlemen of Verona is performed at the theatre and Will is paid for his services. Also, he secretly meets his cousin Father Southwell, who proposes a dangerous collaboration, that Will help him finish writing his treatise to the queen about Catholics attaining religious freedom.

Riding the coattails of his new fame, Will allows Marlowe to introduce him to London's social elite. But, the frolic takes a macabre turn when he partakes in astronomer John Dee's divination ritual. Alice learns the truth about the secret manifest. Will is taken in for questioning by Topcliffe, who intends to use Will as a weapon in the war against the papacy by having him write an anti-Catholic play to counter Southwell's propaganda.

An unexpected arrival by Will's wife Anne sends Will's world in London spinning out of control. He has to choose between his family and Alice. Meanwhile, Marlowe has a transcendental experience through Kelley that leads him to deal with his past. Later, Topcliffe deciphers a code about former Catholic queen "Bloody Mary" that puts Will into a life-and-death situation. He is forced to warn Father Southwell of the executioners' men coming for him.

Will and Alice try to keep it professional by collaborating on a prequel to Henry VI, but their lust returns. However, after Alice calls off her marriage to the rich Keenan Cooper, Will must put an end to the affair. Meanwhile, Anne tries to adjust to London life, but it's not so easy. Later, Marlowe confronts the death of his lover. Presto is put to work in the brothel and faces Topcliffe and tragedy.

After the theatre nearly burns down, Will must help fix it, along with Burbage's debt. Will enlists the help of socialite Emilia Bassano, who introduces him to the wealthy Lord Fortescue. He hires the troupe to perform Will's new play Midsummer Night's Dream for his love. Later, Alice, distraught over Will's rejection, seeks purpose from Father Southwell. Also, Marlowe "sells his soul" by seeking out the Devil during Kelley's ritual, which inspires him to write Doctor Faustus.

After another Catholic becomes a martyr, Will writes about Topcliffe's life by disguising the torturer's evil actions in a play: Richard III. Meanwhile, Marlowe's mind-trip to Hell not only diminishes his ability to write, but also leads him down a self-destructive path. As Will discovers Alice's passion to follow Southwell's cause, he must repay his debt to Marlowe by introducing him to the man himself. Later, the plague continues to wreak havoc in London, causing Richard's best friend and fellow player, Autolycus, to fall ill.

Richard returns from the plague house unharmed, but without Autolycus, and he refuses the role. In order to get Richard to play the king, Will must finish Richard III and make the monstrous Topcliffe more human to the audience, so he confronts the torturer about his childhood. Meanwhile, Marlowe looks for faith with help from Southwell. Later, Alice gets more embroiled in Southwell's plan for religious peace and she is baptized. When the ceremony is interrupted by the queen's men, she puts herself in the dangerous hands of Topcliffe.

Will rescues Alice with help from Justice Young, but it comes at a cost. Will's secret is out to the Burbages, but he convinces them to continue with the play and gets Topcliffe to the theater. Marlowe finishes Doctor Faustus and makes peace with his lover Tommy. Richard III is a success and the main character's being modeled after Topcliffe causes him public shame. He is stripped of his power by Walsingham, the queen's secretary, who was in the audience and saw the reaction. Alice journeys on a separate path from Will by setting sail with Southwell.