The whole setup is to get David to install the cyberskeleton and use it to get his team out. Faraday uses Lucy's phone to fake being her and tell David to install it.
Lucy uses her monomolecular filament to escape just long enough to tell him it's a trap.
It's too late; the only way out is through.
Only automatic injections of neural stabilizers keep him from going psyco.
But once he's broken through the trap, he rallies his crew to rescue Lucy and get revenge on Faraday.