They meet again in Season Four but Bellamy shows anger towards Echo, and Echo doesn't trust Bellamy. He stopped her from cheating during the Final Conclave, which cause her to get banished from Ice Nation by Roan.
Later in "Praimfaya", Echo tried to kill herself but Bellamy was able to stop her and convince her to go space with him. She decides to go to Go-Sci Ring with Bellamy and the others.
In Season Five, Echo and Bellamy begin a romantic relationship.
In Coup de Grâce, Bellamy and Echo meet for the first time in the Harvest Chamber inside Mount Weather. Bellamy is thrashing around in his cage until Echo, who is in the cage next to his, tells him in Trigedasleng to be quiet because they take the strongest individuals first. Bellamy tells her that he doesn't understand what she is saying to him. Echo realizes Bellamy is a member of Skaikru, then spits on him. Sgt. Lovejoy and a doctor enter the chamber and plan to take Echo for a blood transfusion, but Bellamy begins to kick around, forcing them to choose him instead. After escaping the chamber with the help of Maya, Bellamy promises Echo that he will come back to rescue her.
In Blood Must Have Blood (Part 1), Bellamy keeps his promise to Echo and releases her from her cage along with the others in the chamber. He tells Echo that an army of their people will soon be marching on Mount Weather. Before Bellamy leaves, Echo thanks him.
Bellamy: "Get up. It's time to go. I told you I'd come back for you. Come on out. Our people are marching on Mount Weather right now." (Bellamy tries to help a prisoner who struggles) "Hey! It's okay. We're getting you out."
Bellamy: "He's trying to get his people to turn on each other. They'll find my friends. I have to bring them here now. I'll send them in groups. You get your people ready to go, but you wait for me to come back. Do you understand?"
(Echo nods; Bellamy starts off but Echo stops him)
Echo: (to Bellamy) "I know how it feels to lose someone you care about to war, but we do what we do for our people. You slaughter us, we slaughter you. That all went away in the City of Light, but it's back now. So here we are."
Bellamy: "We'll give you guns and show you how to use them."
Echo: "I betrayed you! Why are you trying to save me?"
Bellamy: "Because, Echo, I'm afraid too. We are about to head to space, where we will be tested every minute of every day for next 5 years. I'm not gonna lie to you. I still don't trust you, maybe I never will, but you are strong. We have a better chance of surviving if you're up there with us. Plus, we may need to throw someone overboard to lighten the load."
Bellamy: (to Octavia) "Let's get something straight. If Echo leaves, I am going with her. She is not your enemy! You don't even know her."
Octavia: I know what she's done. Gina at Mount Weather. Ilian in the Conclave! Me on that damn cliff!"
Bellamy: "We all have things to answer for. Things that shouldn't be forgiven, but are, because we did them for our people, our family. Echo is no different. She was an Azgeda spy, but now she's with me, your brother, who is trying very hard to understand who you are now, compared to who you were 6 years ago. All I'm asking is for you to do the same."
Echo: "We've been through this. You're not going with me."
Bellamy: "Like hell I'm not. We survive together, all of us, like always."
Echo: "You are not dying for me, and neither are they. Your sister needs you here, Bellamy. She's fighting and enemy she can't beat, and now Diyoza's using the fact that her people know it to pull them apart."
Bellamy saved Echo first, when Mountain Men tried to take Echo from her cage to take her to the Harvest Project, but Bellamy banged on his cage to make them think that he was stronger so they took him instead. Later, Echo saves Bellamy by stopping Sgt. Lovejoy when he tried to stab Bellamy by holding his hand while Bellamy choked him to death.
In the beginning of Season Four, it was also implied that Bellamy still blamed Echo for the death of Gina Martin, and as Bellamy was about to leave Polis, Echo presents the King's seal to Bellamy. She asks him if they will ever trust each other again, to which he replies, "I doubt it." It was implied that Bellamy is still upset at Echo and shows hatred towards her for betraying him in Season Three.
In "Praimfaya", they are no longer enemies, they become allies and go to space together along with others.