How to Free Shadowheart

Navigate through the Nautiloid ship until you reach a circular room containing a Mind Flayer Pod on the northern edge (roughly x=0, y=346). This pod contains Shadowheart.

If you are a Wizard or Warlock: Investigate Shadowheart's pod. You can pass an Arcana check (DC 7) on the pod and a nearby console to free her. After succeeding, inspect the console to the east of the pod. You will get an option to inscribe the device with glyphs sensed from the pod's warding runes. You can attempt a subsequent Arcana check (DC 10) to examine the powered-up console, but it is not required to open the pod. After this, select 'Place your hand on the console.' You will then need to pass an Illithid check (Wisdom DC 2) to will the pod open.

If you are not a Wizard or Warlock: Proceed through a fleshy door to the east into another chamber. Make your way to the eastern edge of this room and search a Dead Thrall on the ground to find an Eldritch Rune. Return to the room with Shadowheart's pod and interface with the console near it. Select the options: 'There’s a socket in the console, shaped like the rune you found. Insert it.', followed by 'Place your hand on the console.' You will then need to pass an Illithid check (Wisdom DC 2) to will the pod open.

Once Shadowheart is freed, talk to her and select the dialog option 'All right then, let’s get going. I’m [charname].' to accept her into your party.