Pack Mule forces New Game+ by design: the flower kunai missions only exist there
Twenty missions land on their own and all 55 demand a second run. Plus four enemies that cannot be obliterated, the ninjas that only appear in the combat trials, and the no-death chapter you get to pick.
And it counts towards NinjaCoin Miner, Need, not Greed, Work Horse, The One Who Obliterates, Shadow Incarnate, required for the platinum.
From 20 to 55: the jump that costs a second run
There are 55 missions in total: 34 tied to a specific chapter and 21 general ones. They are enemy hunts, specific objectives and combat challenges, and they pay out health items and ninja credits, which is what you need for two other trophies.
Ninja Stuff — 49.9%. Complete 20 missions. Twenty out of fifty-five land almost on their own while playing the story.
Pack Mule — 16.99%. Complete all 55.
The problem is not the missions themselves, it is that some only exist in New Game+ — the flower kunai ones — so this trophy forces a second run by design. There is no way around it, and it is not a planning mistake on your part: it is built that way.
Make use of that second run: it is also where the four remaining health items for The Ninja's Fortress and boss trial number 14 come from.
The other two resource trophies land on their own:
Credit Opulence — 73.31%. Earn 100,000 ninja credits. They come from everything: enemies, missions, purgatory gates and trials, and it is a figure you reach without trying.
If you are going for the platinum you will have a surplus — boss trials pay tens of thousands each — so spend them on crimson blood items, which recharge the Ki gauge: on Master Ninja they are what sustains a long fight.
Need, Not Greed — 79.18%. Obtain 30 items. Any item picked up or bought counts, so there is nothing to hunt: it comes from playing. If you are somehow short at the end, shop purchases count, and by then ninja credits are in surplus.
Pack Mule cannot be closed in a single run: the flower kunai missions only exist in New Game+.
36 enemies to obliterate and four you cannot
Master of Obliteration — 20.59%. Obliterate every enemy in the game.
Obliterating means severing an enemy's limb with your attacks and then finishing them with triangle at point-blank range. Killing them any other way does not count: the limb has to come off first.
There are 36 story enemies plus the Black Spider ninjas, who only appear in the combat trials: without going through those, this trophy cannot be closed. It is the requirement people discover late and that forces a return trip.
And four types cannot be obliterated — Burabura, the Tsukumo variants and Eltus — so do not hunt them or waste attempts on them.
Keep the list at hand: several enemy families have variants that count separately, and that is the usual reason for ending up one or two short of the total without knowing which are missing.
Shadow Incarnate — 59.54%. Complete any chapter without dying.
Chapters 00 and 14 are excluded for being too short. Any of the others will do, so pick the shortest and do it on the lowest difficulty: difficulty is irrelevant for this trophy.
It replays through chapter select without limit, so if you die, restart and try again at no cost whatsoever. It is by far the cheapest skill trophy on the list.
The trophies involved
Each one links to its section inside the full Ninja Gaiden 4 trophy guide.