When Emily was grabbed by a Tree Creeper, she pulled the dagger out of a concealed hiding spot in her boot. She then stabbed the creature's tail forcing it to let her go. She fell to the ground and landed unconscious. Later in a hospital, Matt asked her about it and where she got it but she did not answer. Matt thought it odd that she carried it, as he thought she was a civilian. As he left, he took the dagger from her, saying that he will "take it for safe keeping" and to make sure she doesn't use it to escape.
At some point Emily acquired the dagger back into her possession.
When Emily was kidnapped by Patrick Quinn, she tried to sneak her dagger out of her boot to cut the ropes that had her hands tied but Patrick stopped her saying, "I've traveled with you for three years Emily, I'd like to think I know all of your tricks." Patrick then left it in the flat.
Whilst on board the HMS Gartside, Abby Maitland noticed that Matt was twirling a dagger and staring at it longingly. Abby realised that it was Emily's. When asked where he got it, Matt replied that it was evidence taken from Patrick Quinn's flat.