Everyone thought you were dead, well that's what they thought, since they never found your dead body, and the last one who was with you when you "died" was Rafe, That's why they think he had something to do with it... plus JJ, it was one of the reasons why he hated Rafe the most

you fake your death so that they would not be in danger, since because of your father several dangerous people were looking for you, you dyed your hair and did several other things, they never knew anything about you again, but you knew everything about they, by Rafe, now you were hiding listening to Rafe and JJ fight

"i don't trust you, you understand, my y/n trusted you, remember what happened to her....you remember!" JJ says the last thing screaming

"y/n was only protecting you guys!" says rafe, JJ just looks at him frowning "and you are so eager to blame me for everything, and you won't even listen to what happened, Dangerous people followed her because of her father, she was gonna die.." says Rafe without thinking

"what-" JJ says but Rafe interrupts him

"y/n faked her death to protect you guys...to protect you..." JJ looks at him pouting a little

JJ just looks at him, John B sees that he was about to cry and hugs him "i miss her....i miss my y/n.."

You were inside Rafe's house, you were living there all this time, Rafe looked up to see you and nod, you looked at him and then went down the stairs