The Observatory overlooking the Thirteen Towers serves as your base. This is where you come to spend time with Elena, building your bond by talking to her - and to fuse materials into new items, enhance your weapons and much more.
Ask her nicely and Mavda the merchant can provide you with all sorts of help and guidance.
You can store items and materials, or take a well-earned rest in your bed.
Elena is suffering, so talk to her and show her she's not alone.