London, 1970. Dr. Richard Malone is a brilliant quantum physicist who, after losing his wife, Anouk, in a car accident, has been sent to the mental hospital Burgess. Previous to this, Richard had been a key part of the Atlantis Project, a project to create the time machine, but he lost his job after he became obsessed with the idea that he could use said machine to prevent Anouk's death (a notion caused by a livid vision of her). Desperate to get out of Burgess and convinced that he can save Anouk, Richard befriends Sutherland, a charismatic terrorist who assures him that they will find a way out.
One night, as Richard recalls the events before Anouk's death which involved her suffering a strange depression in the middle of a New Year's Eve party, he is visited by Anouk, who tells him that he doesn't have to save her but that she needs his help. Confused and conflicted, Richard suffers a mental breakdown trying to convince himself that she is not real, causing nurses to interfere and Anouk to disappear that night. She returns the next one and as Richard takes this new encounter more calmly, she reveals that she is not Anouk, but Anjana, and that she is, as a matter of fact, a time guardian trying to prevent the end of the world.
To convince Richard, Anjana proceeds to tell her story. Once a peasant in Middle Age Italy, she was accused of witchery and only managed to survive after being rescued by Elenore, a time guardian, and her father, Gideon, who leads the time guardians also known as The Men from the Time Between the Stars. As Gideon and Elenore took her with them, offering a place to live, Anjana was forced to become one of the said guardians, who are known for their extreme violence and cruelty. The reason for this lies in the fact that, ever since time travel became an option for humanity, there have been countless people who have tried to change the past, thus creating pain and suffering for millions of people.
While reluctant at first to become like them, Anjana changes her mind after Gideon shows her how the peasants brutally killed her father during her escape, and, with the help of Elenore, who also became her lover, Anjana turns into a perfect assassin. Years went by and, much like her companions, Anjana lost her humanity given her violent environment and access to all there is to know. Much like the rest of The Men from the Time Between the Stars, Anjana knows how everything was created and how it will all end as so the futility of human existence.
Things took a turn when Elenore convinced Anjana to go visit the village, she used to live in to get revenge on the peasants that killed her father, and Anjana witnessed the pain her actions caused on a little girl who is then killed by Gideon himself as there can't be proof that he and his people exist, nor anything that could change the course of history. Disgusted by what she became, Anjana tried to convince Gideon to change the purpose of their mission not to kill those who try to change the past, but to prevent time travel from ever existing. As Gideon rejected such an idea, Anjana decided to escape to do it on her own. She faked her death and infiltrated the Atlantis Project (the project that will make the power of time travel possible) by posing as Richard's wife.
When Richard asks why him, Anjana explains that it was the only way without making major changes to the timeline as Richard would indeed fall in love with a woman named Anouk who would then get killed in a car accident, driving him mad. As Richard hesitates whether or not their love was ever real, Anjana admits that it was, and that, at one point, she even considered dropping her mission and leading a happy, calm life next to him before she encountered Elenore in the New Year's Eve party in which Elenore pointed out that if she changed Richard's faith, her cover would blow and made The Men from the Time Between the Stars go after her (thus causing her depression).
Anjana apologizes for causing so much pain to Richard but explains that she needs his help as what will create all the problems related to the power of time travel is the failure of the Atlantis Project, which will be caused by the presence of spies in it. While doubting his fighting abilities, Richard agrees to help Anjana and they leave Burgess.
Anjana trains Richard for a couple of months in which they once again become close. Richard asks her what was supposed to happen with him in the original timeline if she hadn't taken him out of Burgess, to which Anjana says that he would get into big problems because of his association with Gideon but not much more.
The day arrives and Richard and Anjana try to prevent the Atlantis disaster but are quickly found and overrun by The Men from the Time Between the Stars. While the Atlantis crew doesn't die tragically as it was supposed to, they all become prisoners of Gideon who turns out to be Sutherland. As Richard asks how is that possible, Gideon explains that the reason is simple it was Richard who would create such a group. Gideon accuses Anjana of hiding information from Richard and offers to kill her (much to Elenore's protests) if Richard wants it so, but Richard asks him to let her live.
The Atlantis crew is taken to Gideon's ship, the Hades. Richard asks Anjana for an explanation and she tells him that the reason she didn't reveal that he was the creator of The Men from the Time Between the Stars is that she was afraid that he would change and become a cruel man, as that was his faith in the original timeline.
As Gideon invites Richard and Anjana to have dinner with him and Elenore, he reveals that all he wants is to be free, which can only happen if Richard becomes the leader of the Men once again. He explains how, in the original timeline, he helped the original Richard to escape from Burgess and create a different time machine and how, after learning that changing the past doesn't change the present, he helped him to create The Men from the Time Between the Stars as well as how the original Richard's obsession to prevent any of that would lead to them having a fight in which Gideon killed the original Richard in an attempt to protect his family. Gideon then became the leader of the Men but, as years went by, got tired of the violence and cruelty and thought of a plan to bring Richard back without making major changes to the original timeline and so he saved Anjana knowing that, because of her kind heart, she would rebel at some point and become Anouk's substitute (thus preventing Richard from losing his wife and, therefore, preventing him from becoming a mad, obsessed man). This information, however, is not well seen by Elenore, who blames Gideon for all the pain his plan has caused her and Anjana and starts a revolt.
Along with Elenore, Anjana and Richard escape and set free the Atlantis crew, then join forces to fight The Men from the Time Between the Stars. Gideon fights Elenore and threatens to kill her if Richard and Anjana don't surrender and take his place as the guardian of time. Richard agrees, acknowledging that his original version was the cause for all the pain Gideon went through, and apologizes to him. As Gideon realizes his actions and the impossibility of changing his sins, Gideon apologizes to Richard, Anjana, and Elenore and kills himself.
As things calm down, Richard takes the Atlantis crew back to their time, warning them about the consequences of their conflicts. The Atlantis crew agrees not to carry on with the project, nor share any of this with anyone for the good of humankind. Anjana then makes amends with Elenore, telling her that she will always be there if she ever needs her and offering a new mission: to help her parents find a peaceful life. Elenore agrees and infiltrates Burgess, where a young Gideon wonders where did Richard go.
Richard and Anjana reconcile and become the new time guardians.