Throughout Season 1, Kate Moreau left a series of clues for Neal Caffrey to find.
Wine Bottle[]
The Wine Bottle
In "Pilot", Neal breaks out of prison to go after Kate when she broke up with him in prison and stopped visiting him. At the apartment they shared, he finds she has moved out and taken all their belongings, save for one empty bottle of Bordeaux '82. Initially, Neal takes the bottle as Kate's way of saying goodbye because it's empty.
Later on, using lemon juice and a candle, Neal was able to find a map leading to Grand Central Station hidden on the label.
Letter[]
In "Threads", Neal shows Mozzie a cheesy love letter from Kate. When folded in a particular way, the letter reveals the following message: "We are being watched".
Security Tape[]
In "Threads", Neal and Mozzie watch the recording of Kate's last visit to Neal in prison, and they realize that she was tapping in Morse Code, spelling "BOTTLE", which is what prompted Neal to go back to the bottle.
Paper Flower[]
In "Bad Judgement", when Peter passes on a message to Kate from Neal, he brings one word back: "ROBERT", which Neal realizes means Kate's late father. On the grave of Robert Moreau, Neal finds a paper flower, which leads him to Alexandra Hunter, who brings him to the music box.