Story progression
There are two different kinds of dialogue; general idle dialogues, which have clickable anchors to interact with Marigold, and story dialogues, which present the user with choices and must be completed before the ghost will return to normal operation.
The story dialogues will only appear once the user has interacted with Marigold enough. Idle dialogues will progress the counter, and clicking on the anchor text within those dialogues will progress it futher, pushing the player more quickly through the story based on how interactive they are.
Shell changes
The story has 6 phases, each of which corresponds to a change in the shell. The changes are as follows:
Phase 0 - The shell in its most basic form, completely static with no facial features, and very transparent.
Phase 1 - The shell becomes a little more opaque.
Phase 2 - A mouth fades in, and from this point on the shell will have talking animations.
Phase 3 - The body becomes a little more opaque, and has now reached its full opacity. It is still somewhat transparent, especially in certain areas.
Phase 4 - Eyes fade in, and are gray in color. From this point on, the shell has blinking animations.
Phase 5 - The eyes fade from gray to orange.
The changes are subtle, and typically happen in the last section or two of the story dialogue that transitions into that phase.
Note that each dialogue has certain expressions planned for it, although these will only show up if the phase has progressed to a point where the mouth and/or eyes are visible. This creates an effect where idle dialogues which are seen in earlier phases may have additional nuance if the user views them again when the mouth and eyes are visible.
When the ghost boots, it will start with the appearance of the earliest phase of the shell, and fade through each phase until it has reached the phase the user is currently on. The full fade-in when booting at phase 5 can be seen in the following gif.