A route that visits all rooms requires at least 69 transitions.

We start by assuming that we have a full route, then count and remove groups of required transitions, along with removing rooms that are cleared (both entered and exited) by those groups and counting rooms that are guaranteed to be entered (but each one not more than once). Note that in many cases a group of rooms can be used either as a loop or as a thoroughfare; the minimum number of required transitions assuming the rest of the route is maximally convenient is what is listed.

We start with 58 rooms, which I'll use abbreviated names for many of because otherwise oh dear. {KC,M,A}{S,M,N} are the three major south-north paths in the King's Court, Market, and Alley. T{L,H,R,G} are the Ladder, Hermit, Rats, and Gate in the Tunnels. SD is the Shining Door. P{S,P} are Produce Storage and Produce Passage.

The groups are as follows:

• Entrances: You start at one entrance for free, but it requires a transition to get out of. The other two require two transitions each. +5 transitions, −3 rooms, guaranteed entry to KCS, MS, and AS.
• Color Maze Loop: From the Safe room, there is only one way to enter the Color Maze, and you must leave by the same path, taking four transitions. It takes six transitions to clear the Color Maze. +10 transitions, −7 rooms, guaranteed entry to Safe.
• Rug'n'Mug Loop: From KCS, you must clear the loop of two rooms to the west and return to KCS. +3 transitions, −2 rooms, guaranteed entry to KCS (redundant).
• Crone End: The only way to clear Brawl and Crone is a backtracking loop starting and ending at SD. +4 transitions, −2 rooms, guaranteed entry to SD.
• Red and Blue: The series of rooms from Grass Corner through Blue Marble Southeast can be treated as a straight path.¹ +8 transitions, −8 rooms. No guaranteed entry can be tacked onto the end because Grass Corner is a map exit.
• Golden Hall: Must be entered and exited. Safe and Grass Corner are already known to have been visited. +2 transitions, −1 room.
• Nooks: PS, Purple Rug Lady, Chained Redshirt, and TL are all side rooms. +8 transitions, −4 rooms, guaranteed entry to PP, MM, AM, and TH.
• Elemental Zone: Has KCS to the west and PP to the east, both known visited. Can be a loop or a thoroughfare but takes a minimum of five transitions either way. +5 transitions, −4 rooms.
• Parrot Way: Has MS to the west and AS to the east, both known visited. +3 transitions, −2 rooms.
• Locust Corner: A required loop, and AS is known visited. +5 transitions, −3 rooms.
• Shawlbeard Cluster: Shawlbeard, KCN, and KCM. Adjacent to Safe and/or KCS, both known visited. +4 transitions, −3 rooms.
• Tunnels South: TG and TR. Adjacent to AM and/or TH, both known visited. +3 transitions, −2 rooms.
• Tunnel Ladders: Must be entered and exited. Adjacent to AM, SD, TH, all known visited. +2 transitions, −1 room.

This is a total of at least 62 transitions to clear (enter and exit) 42 rooms. An additional 9 rooms (KCS, MS, AS, Safe, PP, MM, AM, TH, SD) are guaranteed to have been visited as a side effect. That leaves a cluster of 7 rooms (MN, Crumbling Corner, Teal Lady, Goat Field, Goat Corridor, AN, Peeking Orange) which is a bit harder to analyze due to the remaining two map exits being in there along with various harder-to-constrain links to their surrounding rooms. Nonetheless each of those 7 rooms will take at least one transition to enter, for a total of at least 69 transitions. This does not prove that a 69-transition route exists, only that a route with fewer than 69 transitions is guaranteed to miss at least one room.

¹ I conjecture that it is never transition-optimal to use the southern east-west door in the Blue Marble Zone, though I haven't constructed a proof; a route where that door weren't easily avoidable would involve using the Blue Marble Zone as a loop rather than a throughfare, and that results in uncomfortable backtracking through Prim Redhead. This may however be of relevance to non-room-complete paths, where maybe you hope that the middle three rooms contain no sheep…

In this thread, I'll be counting room transitions starting from and including the click on the door out of the entrance room, up to but excluding the click home. This corresponds to all room transitions that are fully included under the current timing rules, given that the first frame of the click home is considered the stopping point.

I count 76 transitions in Kjorteo's current 6m56s900ms 100% (Hardware) run, using a route that starts in King's Court and zigzags north-south-north while going west-east, with a detour into the Elemental Zone. In my own current 4m21s467ms 100% (Emulator) run, I count 78 transitions (including some substantial navigational mistakes), using a route that starts in the Alley, then goes north along the Market corridor and south along King's Court before crossing back east. I did this without a map at the time, and there are some paths I thought were closed that seem to not be.

I believe a route with 72 transitions is possible starting from the Alley Entrance:

1. (1) N to Alley South.
2. (5) E SE N W W to clear Locust Loop.
3. (3) W W W to clear Parrot Way and reach Market South.
4. (2) S N to clear Market Entrance.
5. (8) NW N S W S W N W to clear the Produce Zone and the Elemental Zone and reach King's Court South.
6. (2) S N to clear King's Court Entrance.
7. (3) SW N E to clear Rug 'n' Mug and Passerines.
8. (3) N E NW to sweep up the rest of King's Court via Shawlbeard.
9. (3) W W W, entering the Color Maze.
10. (6) W W N NE E S to loop around the Color Maze.
11. (3) E E N to reach the Golden Hall.
12. (5) N E E E E past the Prim Redhead and entering the Blue Marble Zone from the west.
13. (4) N E S S to clear the rest of the Blue Marble Zone and re-enter the Market at Market North.
14. (8) S W E SE N N E E to clear out the rest of the Market and traverse the northeast passage to Alley North.
15. (3) S W E to grab Chained Redshirt and prepare for the final stretch.
16. (7) SE E N N S W N to swing through the Tunnels and reach the Shining Door.
17. (4) N E W S to clear out the northeastern L and return to the Shining Door.
18. (2) W N to reach the last lousy room and wave goodbye to Peeking Orange on the way home.

This takes the western half of the map in the opposite order from my last run and avoids some backtracking in the Market/Alley crossovers.

I didn't mean manually, if that's what you were thinking! I was thinking throw the video into a program, verify by having it generate an overlay that you can rewatch with. I thought some of the discussion earlier involved other games (New Super Mario Brothers and Sonic '06, I think?) where a timing source that excluded load times was used…

A separate possibility that occurs to me here is whether postprocessing could be used to exclude room transition time entirely, by counting only frames on which the yellow cursor appears. 🤔

Hmm, “Goat Corridor” and “Goat Corner” are too close to each other, too. Goat Corridor and Goat Field, maybe?

I like “Tunnel Hermit” as more specific imagery and will switch to that (I won't edit the above post for new names, but I'll edit if I turn this into a guide later). Your interpretation of Muddy Blue Guy feels compelling to me too, but I can't think of a good name to switch to OTTOMH; “Potter” has distracting pop-cultural connotations now. Maybe I'll think of something later. And yeah, I feel like the fire room is pretty ambiguous about whether it's a heating fire, a kiln, a culinary oven (food also goes in bowls, after all)…

I like “Tunnels” a bit better than “Sewers” because the default image of the latter in the 21st century has implications that I think you don't quite find in CD-i Nineveh and that aren't well-represented.

I think the tall vs short room distinction is actually relevant from a gameplay planning perspective! Even if they're all “one screen” in a purely mechanical sense, having multiple exits to the sides changes the effective navigational feel a lot, and it does fit the way you put them on a grid as far as the actual connectivity goes; I wouldn't be surprised if the game designers had drawn a similar map when making the areas. The only quibble I have with the distinction as made on your grid map is that you draw Market South as three tiles tall, whereas I think it makes more sense to merge the two trouble exits to the west and make it symmetrical with the other two major areas.

When I was plotting out my own run, I gave all the rooms names, some of which were better chosen than others. Here are my current suggested names for them, in case it helps with discussion of strategies. Some of this makes reference to Kjorteo's map (https://www.speedrun.com/the_story_of_jonah/guide/ari1g), though it should be comprehensible without it.

There are three major areas: King's Court, Market, and Alley. (Rationale: “Marketplace” is too cumbersome and “Market” is very similar in flavor, while “Court” or “King” are too far from the in-game labeling to be easy to remember. This is the same light modification used in Kjorteo's map.)

The interface consistently presents the viewpoint character as facing in the same direction; you cannot turn. We call this direction north (again the same as in Kjorteo's map), resulting in west and east being to the left and right sides of the screen and south corresponding to the reverse arrow.

Each of the major areas has a stub entrance at the south with only a north exit, followed by a three-room corridor from south to north with several other exits along the sides. These are all called ‹Area› Entrance, South, Mid, and North. Market North and Alley North also have north exits, but those lead to rooms with a substantially different visual style. Market South may also be known as Red Fez due to the prominent NPC with a red fez, red clothing, and gold tooth.

The Color Maze is effectively part of King's Court topologically but is useful to consider on its own. Its six rooms are all named Maze ‹Color› aka the ‹color› maze room. The colors form a six-color rainbow in counterclockwise order: Red, Orange, Yellow, Green, Blue, and Violet. The exit is east from the yellow room.

A “short” room takes up one cell on Kjorteo's map. A “tall” room takes up more than one cell from north to south; there are no wide rooms.

West of King's Court South is a two-room group containing Rug 'n' Mug to the south (scattered colorful rugs, sitting NPC holding a cup with green stalks sticking out) and Passerines to the north (colorful small birds on the ground).

East of both King's Court Mid and King's Court North is Blue Shawl aka Shawlbeard (NPC with blue shawl, large dark gray beard, and shadow over face).

East of King's Court South is the Elemental Zone, a four-room square containing Bowls to the northwest (colorful bowls on the ground), Fireplace to the northeast (stone enclosed fire, fire sounds), Muddy Blue Guy to the southeast (NPC with scruffy beige hair, blue hat and apron, prominent mud stains), and Water to the southwest (water sounds, two apparent north exits of which only the northwest one is valid).

West of Market Mid is Purple Rug Lady (NPC with golden nose ring and blue hoop around neck carrying a bright purple rug with golden trim, window with fake sheep, trouble stairs west).

East of Market Mid and Market North is a two-room group containing Crumbling Corner (short, trouble bricks with hole east) to the south and Teal Lady (round NPC with teal dress, cane and closed eyes) to the north.

North of Market North is the Blue Marble Zone, a four-room square containing Blue Marble Northwest (growling dog, owl), Blue Marble Northeast (owl), Blue Marble Southeast (bare), and Blue Marble Southwest (“King's Court” sign, golden figurine). These all have blue textured walls.

East of Alley South is a three-room cycle containing Locust Junction to the west (thin round-faced NPC with green robe and belt), Locust Corner to the southeast (ceiling joists, curtain north), and Locust Stairs to the northeast (the iconic locusts, window north, trouble stairs east).

West of Alley Mid is Chained Redshirt (NPC with shackled wrists holding a long stick-like object (possibly a broom) that extends off the bottom of the screen, curtained window).

East of Alley Mid is the Tunnels, a five-room group with prominent frog sounds. The main four-room inverted-C shape contains, in clockwise order from northwest, Tunnel Ladders (ladders north and west, trouble hole west-down), Tunnel Guy (NPC with sparse, white, pointy facial hair and pale green loincloth, carrying a red sack), Tunnel Rats (black rat north, white rat and trouble exit east), and Tunnel Grate (grate west). North of Tunnel Guy is the stub room Tunnel Leaves (scattered leaves on the ground).

East of Alley North and north of Tunnel Ladders is Shining Door (door north with light coming through), which is the first room of a dead-end three-room L group containing Shining Door, Brawl (shouting sounds, angry NPC partially through north trouble door), and Crone (NPC with pale purple shawl, light green shirt, and folded hands, dark window north).

North of Alley North is Peeking Orange (thin NPC with orange clothing and white beard leaning out of a curtained trouble passage west, direct view of home).

Between Market South (west) and Alley South (east) is a two-room corridor containing Parrots to the west and East of Parrots (“Market Place” sign) to the east.

Between Fireplace (west) and Market Start (east) is a two-room T junction containing Produce Passage (the room that must be passed through, “King's Court” sign, trouble hole) to the south and Produce Storage (stub) to the north. These both contain boxes of some kind of fruit or vegetable.

Between the Yellow Maze Room (west) and King's Court North (east) is a two-room corridor: Orange Hats Guy aka Maze Guy (NPC near camera with elongated face and two orange hats) to the west and Safe to the east. North of Safe is Golden Hall (several trouble exits).

West of Blue Marble Southwest is a long outlying passage with the western exit. From east to west, these are Back Entrance (“Market Place” sign), Prim Redhead (small NPC with blue and white hourglass dress, poofy red hair, and feet pointed apart), Patio Corner (long, view of home through bars north), and Grass Corner (direct view of home, no floor, grass extends to bottom of screen); Grass Corner connects south to the Golden Hall.

West of Alley North is a two-room corridor containing Goat Corner to the west (direct view of home) and Goat Corridor to the east, both with visible goats (Alley North itself also has a visible goat). Goat Corner connects south to Teal Lady.