Unsurprisingly, it's quite a bit of work to reverse-engineer something you have absolutely no info on (e.g. in computer programs you at least know OS API calls the program makes, and can use that as a starting point), especially when you're learning both the hardware and the assembly language as you go. Ultimately, it took me an embarrassingly long time to get the job done (certainly more than it was worth), and I ended up disassembling a lot more of the game than was necessary (as is often the case when you don't have any idea what you are looking for). I'll just talk about some of the more important lines of investigation, findings, and complications.
As I didn't know anything about the game, naturally the first thing was to hit "step into" and see where I ended up. I always ended up in the same place: a busy loop that checks a single value. Given the nature of this and some idea about the hardware, I reasoned that this was a loop to wait for the next vertical sync, to start on the next frame; this was confirmed by observing that address being written to from the non-maskable interrupt (vsync) handler.
From there I stepped out of the function and took a look around, writing down the various functions called after vsync. I then went about refining the list and detailing more levels of the call tree, ultimately (after all of my disassembly) resulting in the call tree and other related notes below (note the comments have a focus on things relevant to finding this pause glitch). One thing of particular importance is that there's an object-oriented handler for each object type, and the appropriate handler is called for each non-empty object table entry.
$E936 waits for vertical blank to occur
$C971: for each object calls $C8DF, decreases hit timer if nonzero, calls $C9A4, and calls $C928
-$C8DF copies object data from $400+$56 to $46 ($C925 writes life)
-$C9A4 sets hit timer back to full and decreases life in the object buffer when hit with hit timer at 0 after decrement
--$EB51 saves the object-specific handler to $7A (LE)
--jumps to the object-specific handler at $C9D3
-$C928 copies object data from $46 to $400+$56
$CA4B->$EA3A->$E61B->$E63C/$EB98 unmaps $8DF6 page [the page the object handlers are], which gets mapped by the NMI handler
$EB7E NMI handler (does not branch)
$EB97 IRQ/BRK handler (stub)
$F7: controller 1 state (bits in reverse order)
$F8: controller 2 state (bits in reverse order)
For a while I did some looking around with breakpoints on the location in the object buffer where the life is stored, looking for things that modify it. Some of the information gathered this way:
Copy of object struct for current object: 46
Buffer used to hold 16-bit pointers [LE] from various tables: 7A
$53 [life of the current object] written to directly by $8DF6 in $C9A4 when damage is taken
$8C6B-8C9F, $8DDF-8DFE (inside $8D76) only executed when hit timer is 0
During pause taking hit, $C1E6->$D7A0 returns A0/N+ to $8DD5 on boss 2, but 7F/N- to boss 5
$D7A0 seems to determine whether you get hit during pause. $7E indicates whether you're being hit or not: high bit for hit, lower bits for damage taken.
$7E is written to by $D71A in ($C141->$D711) when hit by boss, $D7B2 to clear hit per frame. $D71A is not reached when paused with boss 5 because $D6CD does not return
$D6CD returns if the current object is hitting the player, throws an "exception" returning to caller of caller if not hitting (returns from $D710)
Eventually I decided to take a more systematic look at the object handler for the catacombs (overhead view) player object:
$8C38->8D98->$8DBF catacombs player object handler paused
-$C0FF->$EF2B sets $3E and $3F to the X and Y coordinates (in pixels on screen) of the player for $D7A0
-$C1E6->$D7A0 returns A0/N+ to $8DD5 on boss 2, but 7F/N- to boss 5, when paused and being hit. A indicates the damage player should take. highest bit of A and the negative flag indicates whether player is hit or not.
-on N+, $C216 then handles hit (including decrease life)
From this we can see that $C1E6 is the switch we're looking for, determining whether the player takes damage; though a look through the function shows a clear lack of anything resembling hit detection - it simply reads from a struct in memory at $7C, generated who knows where. So, if that isn't determined in the player object handler, maybe it was handled in the objects you can be hit by. For that reason, and to satisfy my curiosity a bit about what makes bosses tick, I decided to take a look at a boss handler function; and as I hate the crab boss so much, naturally I went with that, first.
It was about this time that I discovered that NOPing function calls was a very effective way to quickly get an idea what a function is doing. This method works poorly on computers, because of the greater number of registers and drastically greater stack usage, making such NOPs result in crashes more often than not. On the NES (or at least in Blaster Master), however, the method works very well, with crashes very uncommon.
Crab (level 5) boss unpaused object handler ($A6D0):
-$A07B: (no discernible effect)
-$A6DE: handles movement of crab and state transitioning (but not animation)
-$A7A2: spawns bubbles when necessary
--$C1F5: spawns a bubble
-$C0FF: updates crab screen position based on crab 65 position (NOPout fixes crab position where it shouldn't be, despite crab 65 object movement). affects everything onward.
-for each body segment (right pincer, left pincer, back):
--$C141->$D711: detection of whether player has been hit. detection of player being hit by green sprite is elsewhere.
---$D6CD: checks for collision
--$C216->$DECC (only if hit)
-$C12C: (no discernible effect)
-$C189: draws (animates?) the green sprite
-$C144->$D697: sets player damage if player hits green sprite. also handles things damaging the boss.
--$D6CD: returns on collision (either player hit by something or boss hit by something). eats the stack frame if no collision (returns to caller of caller)
-$9EB3: animates the background layer
Okay, so $D6CD is another function that looks like a good candidate. So, let's take a look and see if it's what we're looking for or another tangentially related function (don't blame me for the formatting, Blogger doesn't like indentations).
$44 = A
$00 = $3E - ($40 / 2)
$01 = $3F - ($41 / 2)
X = 0xF
A = $7E[X]
if (A > 0)
$45 = A
A = $7C[X] - $00
if (A <= $40)
A = $7D[X] - $01
if (A <= $41)
X -= 3
} while (X >= 0)
Now that looks like a collision detection function, more or less. We can see the X coordinate, Y coordinate, width, and height of whatever it is we're comparing against at $3E-$41, respectively (this is a case of a memory region being used like a stack frame). We can also see an array of 5 structs containing the X coordinate, Y coordinate, and a thingy, respectively, starting at $7C. Clearly only the size of the "current" object is considered, and the array of thingies are just points.
Well, let's think about it for a minute. We know that this function is called 4 times for the crab boss, for the 4 different parts of the body (and that one of those is not like the others). What might collide with the boss that would be of interest? Well, the player and the player's projectiles. A bit of playing around proved this to be true: the first entry in the array is the player, the rest are the player's projectiles (limited to 4, as you can see). That third byte in the struct array indicates the amount of damage the projectile does (or 7F for the player).
So, now we have everything we need to figure out how this works. The boss object checks for collisions with the player and the player's projectiles. If it hits the former, it marks the player for damage, which is then applied by the player object handler (presumably next frame, since the player handler always gets executed before enemy handlers); if it's the latter, the boss takes damage, though only if the part hit is the green sprite, which is the hit box.
Now that we know how the collision detection and damage system works, and why bosses that are susceptible to being hit while paused also themselves can hit you while paused (the collision detection for both is one in the same); that just leaves the question of why it only operates on some bosses. Well, it was about here that I discovered that that wasn't actually true. While only some bosses can be hit (and hit you) while paused, this is not the case for projectiles. Specifically, the projectiles fired by boss 3 and boss 8-1 can hit you while paused, even though the boss cannot be hit while paused.
Well, it turns out there are two sets of object-specific handlers, one for when the game is running, one for when it's paused. Now, bullets and other things are generally not prone to the problem of dealing damage while paused, as they disappear as soon as they hit something (e.g. the bubbles spewed by the crab boss). The things that can hit you while paused appear to be exactly those objects that have pause handlers and that don't disappear after hitting you; this is the case with all susceptible bosses, plus the projectiles of bosses 3 and 8-1.
Boss object handlers:
1 (63): base $A58A, paused stub
2 (5F): $9B64
3 (61): $A196, paused stub
4 (5D): $970C
5 (65): $A6CD, paused stub
6 (5F): $9B64
7 (5D): $970C
8-1 (67): $AA34, paused stub
8-2 (69): $AC84, paused stub
While I didn't go searching for every single object handler to compare the paused and non-paused versions, I did compile a list of the ones for the bosses. Note that there is only actually a single table of handlers in memory; the address in the table points to the paused handler, while the unpaused handler is always 3 bytes afterward (3 bytes is the size of a JMP instruction). For the bosses not prone to this glitch, you can see that I've indicated the pause handler is a stub that returns immediately. For the rest, the pause handler jumps midway into the unpaused handler (after things like movement).
To illustrate this, take a look at the handler for boss 2 ($9B67):
-$A07B: (no discernible effect)
-$C01E: handles movement of boss
-if time to spawn next projectile:
--$C1F5->$D851: fork projectile from boss, giving it a new proto-object type
-paused handler jumps directly to here
-$9D77: draw and do hit detection for arms
-$C090->$D770: do hit detection for back (not hit box)
--$D711: hit detection
-$C093: do hit detection for hit box
-$9EB3: moves and animates the background
So, that's how it is. Now we know why it happens and why it only affects some things. That just leaves one more question: is it a bug or a feature? Unfortunately, the evidence is much too ambiguous to answer that clearly. While it's within the bounds of imagination that damaging the boss during pause could have been intentionally put in as a cheat of sorts, it's very hard to imagine that the same thing against the player would be intended.
Yet it's also hard to imagine that it could be a bug; while the player being hit during pause could be eliminated by a single change to the player handler (a single mistake, in other words), doing the same for bosses would require that every boss's handler be changed. Furthermore, there's the fact that only 2 of the 5 unique boss object handlers (2 of them are used for 2 bosses each, bringing the total to 9 bosses) have pause handlers, in contrast to the player and most projectiles, and without pause handlers the bosses don't even get drawn completely (and what point is there in having a pause that lets you see the boss battle if you can't see the boss?). It seems as though a lot of stuff was left out or in arbitrarily; I have to wonder if there is a deadline lurking in here, somewhere.
Various resources used during reverse-engineering:
Nintendo Entertainment System Documentation
6502 Instruction Summary
How NES Graphics Work
Comprehensive NES Mapper Document
For more info, see this big list of documents