Emulator used: FCEU 98.12-blip
Aims for fastest time
Takes hits to save time
Abuses programming errors (clipping)
Manipulates luck
Please note: the checksum will not match if you use Ninja Gaiden (U), the rom used by the previous published version. However, I've checked and the run will still play just fine. My version of the rom isn't labeled (I'm still not sure which version it is so I've listed US, which I've tested it with) and I didn't realize it was the wrong one until I was already somewhat far into the run. Luckily it doesn't seem to matter which is used at least on my end. Hopefully there's no problems in this regard.
This run is 276 frames (4.5 seconds) faster than the published version. First let me say that there's no way I'd have been able to make a run this fast without BoltR's previous one as a guide. His run is very good and there are a number of spots where I just copied his technique as closely as possible. However, obviously I made some improvements as well.
The largest one, and the reason I started the run in the first place, is on 3-1. BoltR's method of picking up the fire wheel (used for the boss) is very slow and I was able to improve it substantially. You'll have to watch to see how. This improvement was worth 108 frames. The rest of the improvement comes from a large number of minor optimizations spread throughout the whole game. BoltR chose to do the run by picking up the minimal amount of power needed for the bosses. Though this is kind of a neat way to do it, it also actually costs time. This is because it forces him to use Down+B. As you may know, when carrying Jump & Slash you can press Down+B to swing normally when jumping. However, to do this you have to let off left or right for one frame to get the game to accept the input. This does in fact cost you one frame of lateral movement. This is not true of ordinary swings during jumps, so when you don't have Jump and Slash, or are out of power, you can attack without slowing down. All these lonely frames add up over the course of the game.
I tried to minimize use of Down+B as best I could, though I wasn't able to get rid of every instance of it. Particularly 2-2 and 4-2, where there are enemies chasing from behind, force you to play it a certain way that requires this move. On other levels I either accumulated a lot of power and used Jump and Slash to attack, or I let it run out and sit on zero until just before the boss. It depends how the level shakes out as to which is best.
As a result of this change (and my personal tastes) the run looks very different stylistically, as I kill many more enemies and am a lot more active in general. I think it's still very entertaining to watch.
Notable spots: All of level 3 is spectacular, in my opinion. The improvement in 3-1 really makes it look crazy smooth and 3-2 is very nice too. I also found a more modest improvement on 5-1 and the level overall is pretty nice. I save a lot of time by taking damage on this and on 5-2, and get very low on health. Also, right at the end of 6-2, I use a different way of getting to the door than BoltR did. Surprisingly, this is only worth 7 frames, but it's a new trick. One other oddity: I gain 21 frames over BoltR on 4-3, but I'm actually a second behind him on the game timer. Very strange.