Not everything will unlock in Spiritfarer immediately, not unless you talk to the correct people. That’s the case for anyone looking to obtain the bottled ectoplasm. You can add it to your collection of things to find by speaking to Stanley. You won’t be able to talk to Stanley until you do quite a bit of fishing, or luck is on your side and Francis arrives with a particular item available for you to purchase.
Fishing will be how you acquire the mysterious seeds that are capable of turning into Stanley. Some players have said there are seeds that Francis, the Mysterious Trader, can sell you, and have reported it works to conjure Stanley. Multiple players have said it works, so it must work both ways. Fishing is probably the most difficult part, so hopefully, Francis brings those seeds to your boat. Regardless of how you receive the mysterious seeds, take them down to your garden and grow into Stanley.
After that, you need to follow Stanley’s questline to obtain the ectoplasm. By following Stanley’s quest, you will eventually receive ectoplasm as a reward for your hard work. You’ll be able to collect it moving forward. Acquiring the mysterious seeds is the toughest part, though. Working with Stanley is pretty easy once he’s on your boat.