In season three, DC’s Legends of Tomorrow face a new existential threat created by their actions at the end of last season. By revisiting a moment in time they’d already participated in, they’ve essentially fractured the timeline and created anachronisms all across time! Our team must find a way to return all the anachronisms to their original timelines before the time stream falls apart. But before our Legends can jump back into action, Rip Hunter and his newly established Time Bureau call their methods into question and disband the team. Challenging the Time Bureau’s authority, they recruit a hacker from the future, Zari Tomaz and continue their time travelling shenanigans, while insisting that however messy their methods may be, some problems are beyond the Bureau’s capabilities. Some problems can only be fixed by Legends.
When the Legends realize that they broke the timeline, Rip Hunter arrives with his new organization – the Time Bureau – to relieve them of duty. The Legends are thrilled to get a chance to put the team back together but a new threat arises when Rory spots Julius Caesar in Aruba. Sara, Nate and Ray devise a plan to steal the Waverider back from the Time Bureau in order to try and stop Julius Caesar from conquering the modern world.
The Legends find themselves in 1870 to fix the anachronism which happens to be at P.T. Barnum's fledgling circus. However, Nate and Ray accidently free a saber toothed tiger, creating a bigger problem. Meanwhile, P.T. Barnum is on the hunt to capture Nate and Ray to make his show even more exciting for the crowd.
When Sara receives a distress call from their “befriended” agent at the Time Bureau, she learns that they have been tasked with going to the future to capture a rogue time traveler. Unfortunately, the Legends make things worse by trying to protect an outlaw named Zari, to hopefully lure in the time travelling assassin. Meanwhile, Stein tries to diagnose Amaya’s condition, but Nate discovers an unusual treatment that Amaya begrudgingly agrees to.
The Legends learn that Ray Palmer will die because they broke time, causing them to race back to 1988 to try and save his life. When they arrive, they are surprised to learn that young Ray Palmer has befriended a time-displaced baby Dominator putting him in harm’s way with the government and the Dominator’s mother. New to the ship and missions, Zari must find her place and learn to trust the team. Meanwhile, Stein begins working on a secret project on the ship which makes Rory and Jax suspicious.
When Nate thinks he has found a pattern to the anachronisms, it leads the Legends to London in 1897 to hunt down a time-traveling vampire. When they arrive in London, they run into Rip, but not everyone welcomes him back so quickly, leaving Sara to make a tough choice in the end. Amaya tries to connect with Zari, but she is still struggling with being part of the team. Meanwhile, Stein discovers what Ray and Jax are up to and is not entirely pleased.
When the Legends track down an anachronism in 1930s Hollywood, they discover it’s none other than a time-displaced Helen of Troy and she’s just started a war between two film studios. As the Legends try to fix history and return Helen to the Bronze Age, things get complicated when they are blindsided by the appearance of a former enemy. Sara contemplates an offer she is made, which would make the Legends leave the anachronisms be. Meanwhile, Stein and Jax find themselves in an unusual predicament.
With Sara out of commission, the team finds a new Anachronism that leads them to the jungles of Vietnam and right in the middle of the war. Ray, Amaya and Zari pose as journalists and trek through the jungle when they are lead to time-displaced Gorilla Grodd. Meanwhile, Nate and Rory run into someone Rory knows which give a glimpse into his past.
Barry and Iris's wedding brings the gang together, but things go awry when villains from Earth-X attack the ceremony. All of the superheroes band together with help from their super friends like Citizen Cold, The Ray, Felicity Smoak, Iris West and Alex Danvers to take on their most formidable villains yet. Earth's mightiest heroes - Green Arrow, Supergirl, The Flash and White Canary - lead their teams into battle to save the world.
Rattled by recent events, the Legends dive into work which finds them investigating an Anachronism in a Viking settlement in the New World. The Legends realize that the Norsemen are worshipping an artifact as their god and are surprised by the artifact’s origin. For the first time, Sara is worried that they might need back up when Damien Darhk shows up. Meanwhile, Jax finds a loophole that could potentially change history, but it is a risk he is willing to take.
After Sara's encounter with Mallus, the Legends are paid a visit by John Constantine, a demonologist detective. The Legends agree to accompany him to a present-day psychiatric hospital and they are surprised to discover who Constantine is trying to help. During the exorcism, Sara, Leo and Constantine go missing, leaving Ray and Zari to try to take care of Constantine's client. Meanwhile, Amaya and Nate once again come face to face with Kuasa.
After the team returns from a mission, Zari finds herself trapped in a time loop that results in the Waverider blowing up over and over again. Zari soon begins to suspect that the answer to stop what is happening might lie hidden among her fellow shipmates' secrets. But in investigating them she starts to understand her place on the team.
When Sara decides to take some private time, the Legends pursue a lead on the whereabouts of the long-lost Earth Totem. Without Sara's knowledge, the Legends find themselves in 1717 to hunt for Blackbeard's long-lost treasure, but in true Legends fashion things go awry. Meanwhile, Ray feels guilty about something he has done and tries to make amends, which lands him in even bigger trouble.
When Damien and Nora Darhrk take Ray hostage they force him to try and fix the Fire Totem, but Ray tries to use the power struggle between them to his advantage. Ray and Nora find themselves working together in 1960's East Germany in order to fix the totem, but soon come face to face with a younger and deadlier version of Damien Dahrk. Meanwhile, Sara seems to be taking positive steps in her personal life.
When the Legends learn that a mysterious tragedy destroyed Memphis in 1954, thus eradicating the birthplace of rock and roll, they embark on their most important mission - to save music. Nate is excited to show Amaya why music is important to him and he is surprised it leads to a rock legend as well as the sixth and final totem, the Death Totem. Meanwhile, Zari helps their newest member try to adjust to the team.