In love, Passionate feelings, Sexual, Made love, Protective of one another, Mary saved him from being hanged, John knows she's a witch, They have a child together, Mary and John joined forces to protect their son, Mary sacrificed her life to resurrect him.
Spoiler warning! This article contains plot details.
John: These are the stubborn facts. And all the love in the world can't change a single one of them.
Mary: Your wrong. Love is stronger than fact, stronger than everything
— about their relationship
The relationship between Salem's most powerful witch Mary Sibley and the hardened war veteran John Alden.
John and Mary fell in love before the events of 1685 but John was sent to join the militia but return's in The Vow seven years later with the sole purpose of being reunited with Mary, only to discover that she is now the wife of George Sibley. The very man that had sent him off to die in the war.
Throughout the first series John is unaware that Mary is a witch and the one behind all of Salem's misfortune but when he discovers the truth in Ashes Ashes he still loves her enough that he wants to be with her.
In All Fall Down they planned to runaway together but their plan was hindered by the witches who used the life of their son to force Mary to stay and complete the grand rite. They are portrayed by Janet Montgomery and Shane West.
In 1685 John and Mary were lovers but he was being enlisted into the militia he made a vow that he would return for her within a year and she would wait for him, each keeping half a silver coin, a reminder of their vow to each other. Several months later, Mary discovered that she was pregnant with his child and sacrificed their baby to Satan so that she wouldn't face the punishment of being pregnant out of wedlock, resulting in her becoming a witch. She waited many years for him but was led to believe that he had died allowing her to marry George Sibley.
Throughout The Salem Series
In The Vow Mary discovers John Alden is alive and has returned to Salem. The couple are finally reunited at church as Cotton Mather preaches to the people of Salem of the new dangers that now plague their town - Witches. Mary seems taken aback to see her former lover but finds her composure and invites John to a dinner party which she is hosting with her husband George Sibley, where later he attracts the attention of the young miss Anne Hale much too Mary's dislike. During the meal John hallucinates of both Anne and Mary caressing him provocatively under the table an illusion created by Mary. He excuses himself wanting some air believing the rich food does not agree with him and finally alone the couple speak. John informs Mary of the reason behind his seven year absence -- he had been captured and tries to convince Mary to run away with him to New York. The couple kiss passionately but Mary tells him its impossible.
In The Stone Child Mary discovers that John has been arrested by magistrate Hale for threatening the selectmen following the death of his old friend Giles Corey. She tries to convince him to leave Salem and lies to him saying she doesn't want him, she watches heartbroken as he gives his half of the silver coin he had given her seven years ago to a beggar girl. They come at odds during Bridget Bishop's trial as he believes her to be innocent but he is unable to save her and both watch as she is hanged. Later he pays Mary a visit and informs her that he is staying in Salem and planning on taking his father's seat on the selectmen board.
In In Vain after Isaac Walton is arrested for attacking the prostitutes at The Divining Rod (due to being under a Witches spell) John goes to speak to Mary and she tells him he has her complete allegiance due to her fondness for the man. She treatens the magistrate Hale but he insists that Isaac must die as he and a accomplice had saw the witches sabbat, she tells John that they plan to hang him and that he must do what ever it takes to save Isaac. Mary cast a spell to trick Isaac into divulging the name of who else had also seen the witches sabbat and is shocked to learn that it was John Alden. Mary keeps this information from the other witches to protect John and saves Isaac after casting a spell on Anne Hale that nearly kills her forcing Magistrate Hale to spare him to save his daughter. She warns John to leave Salem as she cannot protect him.
In Survivors Mary shows jealously as she watches Anne flirt with John at the party held to celebrate him joining the selectmen board. Later that night John is approached by Tituba and informed that William Hooke has threatened her mistress; saying he will spread lies about her unless she get's him access to the ship that is under quarantine at the docks because it contains package that he needs to collect when in actual fact he has blackmailed her that he will inform Salem that she is a Witch; knowledge he had obtained from George Sibley. John confronts Hooke who threatens to tell everyone that he is a murderer but John proceeds to strangle the man to death to keep his secrete. After John has disposed of the body, he speaks with Mary and they talk of the vows they had once made to each other, he asks if they were lies and she tells him they were wishes made by people who knew nothing of the world.
In Lies Mary discovers from Tituba that John is a murderer and has killed again to keep his secrete she goes to the Alden house and pleads with John to tell her it's lies but he tells her that it is true -- he killed twenty men. she tells him his secrete is safe as she is the only one that knows and the couple kiss passionately.
In The Red Rose and the Briar John has obtained the Malum and captures the Witch Rose Browning with the help of Cotton Mather. They take her to the woods to question her but she escapes after casting a spell forcing the corpses in the crag to attack them. She is found by Mary who discovers not only was it Rose who planted the idea into George Sibley head to send John to die in the war but that his life is endanger. She gets her new progeny Mercy Lewis to behead her to save John's life.
In Our Own Private America Mary decided's to dream walk so that she can discover the location of the Malum which is in the hands of John Alden. Despite Tituba's warnings about meddling with any man's head she goes ahead with her plans and John is plagued by sex dreams of himself and Mary which leaves him weaker by the day and in a constant state of arousal but even when she discovers the location of the Malum Mary continues to visit John's dreams nearly risking her own life when she loses control. After their last shared dream they give into their passion for one another when John barges into Mary's bedroom kissing her passionately and they nearly have sex but Mary finds the strength to stop things before they go too far, leaving John confused when she tells him to leave as she has gotten everything she needed from him.
In Departures John kisses Mary passionately and tries to convince her they belong together but she tells him that despite her own personal desire what had transpired the previous night could never happen again as she is now a married woman.
In Children Be Afraid John is helping Anne at the orphanage and is seen by Mary and he is surprised to learn she wants her husband returned to her from Increase Mather's care.
In The House Of Pain After Tituba is arressted and tortured by the hands of Increase Mather she acusses John Alden of being a Witch and Mary is forced to watch helplessly as John is arrested by the selectmen for witchcraft.
In Cat And Mouse folowing the accusations from Tituba that John Alden is a witch, Mary convinces Increase to put his case to the board so she can secretly exonerate him with the help of magistrate Hale but her plan fails as Increase uses her husband to vote instead of her. She offers to help him escape but John refuses to run so she is left with one last option kill Increase with the help of Mercy Lewis who is in hiding after Tituba told Increase she herself was now a witch but the plan fails leaving John Alden life hanging in the balance.
In Ashes Ashes Mary is told by the elders that John must die to complete the grand rite as saving him will reveal to him what she is -- she is forced to watch him go to trial and it is revealed by Increase at court that he has killed twenty militia men as he had been told this by Tituba during her torture. As more evidence is brought to trial he is sentenced to hang but Mary is convinced by Isaac to save John and visits him in his cell. John tells Mary he is willing to die for his crimes as he is tired of living without her. They kiss and Mary transports them to the woods showing John she is a witch.
In All Fall Down John is shocked to learn that Mary is a witch but still loves her and asks her to come with him, she tells him she must go back to Salem but will return when the moon is at its highest. She goes to see the elders and tells them she is leaving Salem to be with John and is never coming back, so Tituba is forced to reveal to Mary the child she sacrificed seven years ago is in fact not dead but very much alive and she must complete the grand rite if she wishes to save her son. With little choice Mary walks away from the chance to be with John Alden and complete's the grand rite killing Increase as the final sacrifice. She is finally reunited with the child that she has mourned for but unbeknownst to her John is gravely injured after being shot.
John: Mary trust me. I will come back for you. Hey look this is all that I have and I swear on my parents grave. This is my vow. This war will not last a year.
John discovered the truth about Mary as a witch in Ashes Ashes.
Although not clearly expressed at the beginning, during the second season we discover that John hates witches and Mary is just another witch to him, as well as Anne Hale. This hatred is put aside when he discovers that they have a child together.
John Alden learned of the existence of their son in Wages of Sin.