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The U.S. Military offers Jack, Richard and the Aerojet team a classified mission that could turn the tide of World War II, but which comes with increased scrutiny of Jack's personal life. As Jack strives to straddle the worlds of mysticism and science, Virgil Byrne's crusade against the Agape Lodge forces Jack and Susan to offer the cult safe haven in their Pasadena mansion, only to have their lives further disrupted by the return of Ernest Donovan, who has come back to Los Angeles more broken than ever.

The Magus invites Ernest to stay at the Parsonage, leading Jack to question both men's motives. Richard discovers that Marisol has been hiding a secret from him that could jeopardize their relationship. In an effort to join the ranks of the Agape, Patty shares a shocking discovery with Jack. And with the new rocketry project already on the ropes, Jack finds help from an unlikely source, Aleister Crowley himself.

Jack's breakthrough fuel formula goes missing from his office, and Jack suspects it was stolen by an enemy spy. As he seeks out Ernest's help to deal with the situation, Susan seeks out the help of the Magus as she attempts to mollify their conservative, upper crust neighbors. When Virgil learns that Patty has also joined the Agape, he turns the screws on Ernest, forcing the broken zealot to choose between loyalty to his beliefs or facing a life behind bars.

Jack's conjuring of the Angel earns Ernest's loyalty but divides the Agape, spurring the Magus to investigate the so-called 'miracle.' Marisol attempts to confront her father about the secret that destroyed their family as Richard deals with his broken heart by diving deeper into the rocketry project. Meanwhile, when Susan's attempt to get Thelema officially recognized as a religion hits a roadblock, she turns to Ernest in hopes of putting a stop to Virgil's harassment once and for all.

Jack sees his ambitions threatened as Agent Wallace grows increasingly suspicious of Jack's ties to Aleister Crowley. In an attempt to clear the air, Jack invites Wallace, General Braxton, and their military colleagues to the Parsonage for a summer dinner party - hoping to show them they have nothing to fear - but his best laid plans go awry as dark secrets are revealed and Ernest takes drastic steps to achieve transcendence.

Following the disastrous party at the Parsonage, Jack loses his security clearance and must strike a dangerous bargain with Wallace to be reinstated. With the police now investigating the Agape, the members' deepest secrets are revealed through a shocking betrayal. Meanwhile, Richard, Chiang and Mesulam are sent to London for a military research project, where Richard goes to great lengths to clear Jack's name. Devastating truths come to light, putting Jack and Susan's future in doubt, and creating the opening that Patty has been looking for.

Susan and Patty's relationship reaches a breaking point when Susan learns of her sister's indiscretions - nevertheless, they must join forces to use Virgil as a means to an end. After Marisol receives devastating news, she gains a new perspective on her relationship with Richard. Jack has a chance to get back into the military's good graces, but the conditions may be too tough to swallow. Yet with the Magus in jail, Jack's power within the Agape rises to new heights; however, the arrival of a new prospective tenant at the Parsonage threatens to change all that. Season finale.