To save Shadowheart in Baldur's Gate 3, you need to find an Eldritch Rune hidden nearby the Mind Flayer Pod where she is trapped. You then insert this rune into the console next to her pod, which will power up the device and allow you to open the pod and free her. Here are the key steps to save Shadowheart:

• When you find her trapped in the Mind Flayer Pod on the Nautiloid ship, ignore the advice to leave her behind.
• Next to her pod is a console that you can interact with. However, it won't open until you find the Eldritch Rune.
• Head to the eastern room adjacent to the pod chamber. There, loot the corpse of a dead thrall to find the Eldritch Rune.
• Return to the console by Shadowheart’s pod and insert the rune. This will activate the console.
• Place your hand on the console and pass an easy Wisdom check (typically DC 2) to will the pod to open.
• Shadowheart will then be freed and can join your party.

If you fail to save her at this point or choose to leave her, she will still survive the Nautiloid crash and can be found later in Act One, but it may negatively impact her disposition and your relationship with her. Saving Shadowheart at this early stage adds a powerful companion to your party and unlocks narrative choices tied to her character.