“Wake Up” begins a pair of people in a person submarine-type craft.They’re near the National City waterfront investigating the crashed spaceship we saw earlier in the season.As they approach it, a beam of light blasts them away.
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Samantha is cooking dinner for Ruby when she gets an idea — she looks down at the pot of boiling water.Before too long, she submerges her hand and to boiling water and doesn’t notice a difference in pain levels, hinting at her invincibility.She orders Ruby to go have dinner at her friends.
At the DEO, Kara instructs Winn to research the ship at the waterfront.He says it’s been there for 12,000 years and it’s made from metal that’s not on the periodic table.Kara, Winn, and J’onn go investigate the ship and J’onn phases the group inside the ship.
They look around inside the ship and are shot at.When the attacker steps into the light, we see that it’s Mon-El — he and Kara embrace.
The group takes Mon-El back to the DEO to run diagnostic tests and find out that he’s able to breathe Earth’s air now.Questioning him, Mon-El reveals the other people in the chambers on the ship are “like him,” passengers on the ship.
The room clears and Mon-El and Kara have a quick talk.Mon-El tells her he’s been trying to send a message to her for seven months.
Samantha drives to a house where a woman named Patricia opens the door.After a talk, we find out Patricia is Samantha’s adoptive mother — she kicked Samantha out of the house when she got pregnant with Ruby.Samantha questions her mother about if she exhibited signs of super powers when she was growing up.Samantha asks for some more information about her birth mother and explains to Patricia how she got shot but wasn’t hurt.
Patricia takes Samantha to a barn on the residence and shows her the pod she used to travel to Earth in.Patricia reveals she didn’t adopt Samantha, she found her crash-landed in the pod.While examining the ship, it activates once Samantha touches it.
James arrives to the DEO to talk with Kara about Mon-El’s reappearance.She admits to James that Mon-El’s been pretty distant since he’s returned.
Samantha is packing her bags to go on a tri by herself.She explains to Ruby that she needs to do it by herself and tells her she’ll leave money for take out since the babysitter’s cooking is atrocious.
Alex tells J’onn to go be with his dad and show him the sights around National City, her and Winn will continue monitoring the sunken ship situation.After getting coffee, J’onn and M’yrnn get into an argument and M’yrnn walks off.
Back at the DEO, a cautious Mon-El surveys his surroundings before unhooking himself from the equipment to snoop around.He’s able to find some sort of weapons room, and chokes out a DEO agent before being knocked unconscious himself by Kara.
Mon-El awakes and Kara’s placed him in on of the DEO holding cells.She ask what he was up to but is unable to get any information out of him.
Samantha’s on the road traveling through a desert, she takes a dirt road and stops to find her car is overheating.
It’s Winn’s turn to talk to Mon-El.Winn approaches him about the alien ship and Mon-El reassures him there’s a lot of stuff he wouldn’t understand.Mon-El asks for Winn’s help to get back to the ship, telling him people — Kara included — will get hurt if he isn’t taken back to the ship.
Kara walks in to the holding chamber to see Mon-El is no longer is his cell.
Wnn and Mon-El are back on the ship, using the item Mon-El recovered in the secure room at the DEO.They turn around Kara to find Kara on their ship.Kara and Mon-El get into a fight, when Mon-El reveals he’s been gone for seven years.When he launched into space at the end of last season, he was sucked through a wormhole and lived in the 31st century for seven years before being able to return.
The pods on the ship begin failing ad one of Mon-El’s colleagues begins drowning in the pod.Kara’s able to step in, break the glass, and rescue the woman in the pod.Mon-El calls her Imra.
With her car broken down, Samantha’s walking through the desert in hopes of find help when the ground starts shaken and rocks start protruding from the ground.When complete, the rocks form a fortress.
Mon-el, Winn, and Kara take Imra back to the DEO to monitor her vitals.
J’onn takes M’yrnn to his apartment and talks about his time on Earth.J’onn asks his father to move into the apartment with him, saying they could make it their new home.
Mon-El is brooding over National City on a balcony when Kara approaches him.Before she’s able to say anything, Mon-El apologizes.They two are talking and Mon-El is about to tell Kara something when Imra wakes up.Mon-El runs to her and they kiss, much to the surprise of Kara.Mon-El tells Kara that Imra is his wife.
Samantha enters the fortress and uses the crystal she took from her pod to place into a whole inside the fortress.As soon as she does so, a hologram opens up and explains that Samantha is Kryptonian.The hologram explains that Samantha’s purpose is to be an “executor of Justice” and calls her a world-killer.Samantha is warned that she’ll soon forget about her daughter Ruby and tell her it’s time for her to become Reign.Samantha doubles over in pain and when she gets back to her feet, her eyes glow red and she says “I have awoken” in Kryptonian.