Madi is the commander though Clarke is trying to stop her from being the Commander to protect her. As Commander Madi has the Flame which contains all the minds of the past commanders and connects their minds to Madi’s including Lexa, Clarke’s greatest love who died 6 years ago.

Clarke and Echo argue

Clarke: Bellamy put the flame in Madi's head.

Echo: He did that to save us all, and she took it willingly, didn't you, Heda?

Clarke: Don't call her that.

Madi: She knows I did.

Clarke: Yeah, because you're brave and reckless and because I was in trouble.

Mad: That's right. I did it because I love you.

Clarke: I thought love was weakness. Isn't that what the commanders in your head tell you?

Madi: Yes, all but one. Madi was referring to Lexa

Clarke: I think you should get some sleep.

MadI: I don't want to sleep. Every time I close my eyes, I see you outside the door at Mount Weather, ready for war, and then I walk away, leaving you there alone. Referring to Lexa’s memory

Clarke: Let me translate that for you. Lexa protected her people by making a deal with the enemy, leaving Skaikru to die, yes, just like I've done here. I don't need ghosts tellling me what I've lost to protect you, Madi.

Madi: Clarke, she's not a ghost. She's real. They all are, and you're wrong about why she's showing me that memory. Betraying you is her deepest regret. She's showing me that because she doesn't want you to make the same mistake she did. Please, Clarke. I know you're scared. I am, too, but I have to do this, and you have to let me.

Clarke: Oh, Madi...This is how we survive.

Madi: It may be...but life should be about more than just surviving. saying this Madi was using both Clarke’s words and Lexa’s dying words against her