Just before exiting the Looking Glass's communications chamber, Charlie hears the signal for an incoming call. He answers it, and when the caller introduces herself as Penny, he calls Desmond. Charlie asks Penny whether she's on her boat, but she denies knowledge of the boat or Naomi. Desmond, meanwhile, notices that Mikhail's body has vanished and comes running to warn Charlie.
Charlie spots Mikhail swimming outside the porthole with a grenade in his hand. Before the grenade can detonate, and before Desmond can enter the chamber, Charlie slams the door shut. The grenade blows open the porthole, and water rushes in. Desmond tries to break open the glass in the door, but it's in vain. Charlie, as the water rises, writes a message on his hand and places it against the door glass. Desmond presses his own hand to the glass to show he understands. The message reads: NOT PENNY'S BOAT.
Charlie makes the sign of the cross on himself and then drowns.
On the island, Aaron cries. Claire comforts him, and Naomi's phone beeps, revealing that Charlie succeeded at his mission.
The title refers to the Looking Glass station and the episode's title—"Through the Looking Glass". It also references the common metaphor for optimism and how good can come from even bad circumstances.
The title may also be a subtle reference to the factual inaccuracy of Charlie's death - the pressurized nature of the communications room would have prevented the water from completely filling it up, leaving it instead "half full," and not killing Charlie.