Arasaka's been working on something called a cyberskeleton. They want David to test it, due to his high compatibility.
Lucky discovered this when she was diving Tanaka's brain. She's been taking out people in the know.
Faraday hires the crew for a job, but it's a trap.
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.