In season six, Waverider co-captains Sara Lance and Ava Sharpe have dealt with monsters, time anomalies, and most recently, villains from Hell, but this time they will face something even more challenging and bizarre ... space aliens! After one of their own is abducted by a ruthless alien, this new mission becomes personal. It will take more than the combined powers of John Constantine, Mick Rory, Nate Heywood, and brother-sister duo, Zari and Behrad Tarazi, to save the world for a sixth time.
After a night of celebrating their beating the Fates, the Legends quickly discover that Sara is missing. Ava sends Rory and Behrad to follow a lead on who can possibly help them find Sara, while Constantine tries to work his magic. Meanwhile, Sara does all she can to try to escape but is shocked to learn who one of her kidnappers turns out to be.
The Legends find themselves tracking an Alien in 1950s San Bernadino and having to figure out what is making the town go on a feeding frenzy. Meanwhile, after crash landing, Sara tries to figure out a plan and runs into none other than Amelia Earhart.
The Legends find themselves in 2045 trying to defeat an Alien warrior which leaves Zari no choice but to enter a popular singing competition. Sara finds herself struggling after being attacked but someone familiar helps her to keep searching for refuge. Meanwhile, Zari and Constantine have a much-needed conversation with each other.
The Legends are shocked when Rory takes command and manages to find the location of an important Alien, but he also lands them in the middle of the Cuban Missile Crisis. The team makes the decision to split up, leaving Nate and Zari to work together to stop a nuclear disaster alongside JFK while Behrad tries to leverage his newfound friendship to stop Castro from starting a war. Meanwhile, with Spooner's help, Rory makes an unlikely deal that could lead him on a solo mission to find Sara.
With Astra now a mortal, she finds it hard to adapt to the real world with no guidance from Constantine. Frustrated and lonely, Astra makes a new friend who promises to help her, but her eagerness for the easy way out could have some real repercussions for those closest to her. Meanwhile, Sara meets the person responsible for her kidnapping and tries to convince others to help her escape.
Mick takes the Waverider and Kayla to try and find Sara, but these enemies find themselves needing each other to survive after landing on the possible planet Sara is being held captive. After a report of an Alien attack, the Legends return to their new headquarters where both Spooner and Astra try to connect to the Alien. Meanwhile, Sara devises a plan to escape by using her charm to win over Bishop.
With Ava a wreck, the Legends make a last-ditch effort to keep Sara from being abducted in the first place, even knowing that it will alter the timeline. Sara grapples with a discovery about herself and is shocked when Rory finds her on the mystery planet. Meanwhile, Spooner envisions what her life would be like if she hadn't joined the Legends.
With everyone finally back together, the Legends find themselves looking to Nate to keep everything calm while in the old West on a mission to find an alien. After trying to keep things normal, Sara reveals her secret to Ava and the team, leaving them all shocked. Constantine looks to Gary who might have the answer to his problem. Spooner and Astra are forced to work together despite their clashing personalities which ultimately helps push them to hone their powers.
Behrad is disappointed because the Legends have forgotten his birthday. Meanwhile, Rory's behavior has been a little off, so Sara and Gary become determined to find out what happened, but Rory gets some unexpected news from his daughter, Lita.
With Constantine obsessed with getting his powers back, he convinces Spooner to join him on the quest to find the Fountain of Imperium. After they find themselves at the end of the Spanish Civil War, Spooner makes an unexpected bond with someone she feels the need to protect. Meanwhile, Sara and Lita are concerned about Rory's health, so they try to convince him to take it seriously.