Every symbol you find under the petals is illustrated twice.

Press the button with the tortoise and holding the button pressed release the key with the tortoise symbol 

Read the message inside the capsule using the ray fish element

Put the holes of the propeller so that you can see the same symbol through the holes. This will result in one of the forms becoming complete (in the circle)

On the released key (with the tortoise on it) you will find a symbol and two arrows.

The decoded message is: atlantic Visit mobilis-in-mobili.net and use this as the password

Similar forms and symbols appear on other elements of the box

The shape of this symbol corresponds with the shape of a slot on one of the sides of Nautilus. 

The contours of the figure key can be found somewhere else on the box

Find the form on the “octopus” side of the Nautilus Cluebox and memorize the symbol inside of the form.

Put this key into the slot in the box as shown, so that the slot on the key hooks a ward inside of the box. Then pull the key and while holding it pulled, release another key

Put the message in the capsule so that it fits in its narrow part. Check whether the ribs of the capsule are in the right position to close it. If not, use the keys to find and adjust the right position   Now close the capsule by adjusting the lid and rotating it clockwise. After