Supergirl kicks off with right where we left off last week as Superman is attacking his own cousin, thinking that Kara is the enemy. Supergirl fights back and learns from Rhea that she used Silver Kryptonite on the Man of Steel who thinks Kara is his worst enemy….General Zod. They use their heat visions at each other before taking the fight into the city. The D.E.O. gets alerted that Kara is in trouble as Alex and Maggie rushes over. The two Kryptonians continue to fight as Kara tries to get Clark to fight through the Silver Kryptonite in his system. Eventually Kara manages to get her cousin back to his senses. Kara wakes up the next morning with Mon-El at her side, but it’s just a dream as Supergirl is actually at the Fortress of Solitude with Superman and Alex. Kara is still recovering from the battle with her cousin as Clark wakes up and is back being himself.
Meanwhile, Lena gets visited by Lillian who lashes out on her daughter for teaming up with someone like Rhea. Lillian apologizes for her recent actions and tries to convince Lena that she wants to be a better mother. Mama Luthor shows Lena the mystery weapon from Lex’s vault as Lillian asks her to make it work in order to save the world. Clark finds out that Rhea used Silver Kryptonite on him as he has never heard of it before. Clark thinks he has a way of stopping Rhea as he uses the Fortress’ database. They all fly back to the D.E.O. as Winn is geeking out about Superman being there. Clark learns about Mon-El and Kara’s relationship as they had never met before. Kara tells Mon-El about the solution that they discovered at the Fortress, but Mon-El freaks out when she brings it up. Back on Rhea’s ship, the Queen gets challenged by the Girl of Steel through a video transmission as she declares for a trial by combat. Rhea accepts the challenge to fight Supergirl.
Mon-El tries to talk Kara out of it, but Superman believes in his cousin and that she can take Rhea on. Alex goes to see J’onn who is still down and suddenly we see Miss Martian by his side. M’gann kisses him as J’onn wakes up and he starts wondering where she is, but Alex assures him that she is still on Mars. J’onn gets informed on what has been going on. Over at CatCo, Cat is furious as she is wondering where Snapper is before Kara and Clark shows up in front of her. Kara starts to explain to Cat that Supergirl asked her and Clark to ask for a favor from Cat. Before they go, Cat asks Kara if she thinks Supergirl is ready for this and Kara thinks she is.
The two cousins fly over to see the Luthors as the two women show them the weapon that will make Earth dangerous to Daxamites when it sends out a trace amount of lead into the atmosphere. Supergirl realizes that Mon-El would have to leave Earth as well. Kara and Clark heads back to the D.E.O. and tell the team about the weapon that the Luthors have at their disposal. Mon-El asks Kara to let her be there when she goes to see Rhea. Kara and Clark decide to spar a bit to get her ready for the battle. Kara gets a pep talk from Clark before she and Mon-El goes to face Rhea. As the two women remind each other what happens if the other loses, Rhea and Kara begin to fight. Kara manages to get Rhea down, but Rhea isn’t playing fair as Daxamite ships begin destroying the city.
Mon-El flies off to stop the chaos in the city, with the help of Superman and Martian Manhunter. Rhea gets punched by Kara once again when she sees Rhea’s face bleed Kryptonite. Over at L-Corp, Winn and Lena are working Lex’s device together. Lillian tries to activate it before Lena reveals to her mom that only Supergirl can turn it on. Mon-El fights off several Daxamite soldiers in downtown while J’onn and Clark fight off a bunch of soldiers on their end. Rhea and Kara battle through the whole city while Superman goes after a ship. At CatCo, Cat and James are almost attacked by a Daxamite soldier before Superman shows up to stop him. J’onn is joined by M’gann who has brought several White Martians with her to stop the Daxam Invasion. Kara gets the upper hand on Rhea before Mon-El shows up and gives Kara the signal to activate the device. Kara activates it as lead is spread into atmosphere. Rhea begins to die as she turns into dust. Mon-El starts having problem breathing as Kara knows the atmosphere is no longer safe for him. Kara tells Alex to get her Kara’s rocket as they fly to a field where Mon-El tells her how much he loves her before sharing one final kiss. Mon-El gets Kara’s necklace before he gets into the pod and leaves Earth, with Kara crying.
Back at the D.E.O., everyone is celebrating the victory while Kara is dealing with Mon-El’s departure. Clark goes to see her as he has to fly home to Metropolis, but comforts her before doing so. J’onn asks how M’gann knew that he needed help as they catch up on what she has been up to. Alex goes out to the balcony to comfort her sister where Kara tells Alex to go and be with Maggie as she should cherish what she has with Maggie. Kara flies off when Maggie shows up from behind to see how Alex is doing. Alex decides to follow Kara’s advice and proposes to Maggie who seemingly accepts it.
The next morning, Kara goes to see Cat who knows that something is wrong with Kara who tells her boss about Mon-El and how their relationship just came to an end. Kara starts talking about that maybe she can’t have it all, but Cat tells her that she is wrong as she believes Kara has accomplished so much and will continue to do so. Kara sees the news that she has to go save the day before thanking Cat as she takes off, as we discover that Cat knows that Kara is the Girl of Steel. Supergirl flies into the city, with a broken heart while we see Mon-El supposedly on his way home to Daxam. But suddenly a worm hole opens up and sucks Mon-El’s ship into it.
The episode concludes with a flashback to 35 years ago when Krypton was destroyed. We see black cloaked figures putting a baby into a pod that is leaving Krypton too. They keep referring to the baby as an “it” that they claim will reign over Earth before the episode cuts to black. There was a lot that went down in tonight’s huge episode that we have to discuss. So let’s go through the top 5 highlights and important moments of the Supergirl Season 2 finale episode: “Nevertheless, She Persisted”