"Someone hacked into Claptrap and left you a cryptic message. You were told that Dr. Ned is not to be trusted, and you can find Dr. Ned's old laboratory by taking a boat off the island. Find Ned's lab and use the secret knock to enter."
Find Ned's original lab to see if he is who he says he is.
Head south to Ned's Infirmary, follow the beach around to the east and you will come to a boat.
Take the boat to Dead Haven (use the transition point). You will arrive at the docks, head up the stairs to the elevator. Take the elevator up.
Fight through the zombies to the secret lab. Enter the lab and listen to the ECHO recorder.
"Dr. Ned is behind the zombies. Imagine that."
If you turn off the console, or come back to Jakob's Cove while playing this mission, sometimes the Claptrap is still tied up, but without rope binding him at all.
The "special knock" you learn from the hacked Claptrap to gain entrance to the secret lab is the first five beats of "Shave and a Haircut, two bits".