system
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human
[Warhammer 40k] How are so few soldiers able to bring whole planets to heel?

I'm reading the series and consistently it's said that the Vengeful Spirit and other Primarch's warships have "thousands" of soldiers aboard.

Even if his ship has 999,999 Astartes, how is it remotely possible to not only subdue a planet within weeks, but leave a garrison behind for conversion?

It's like one Astartes per hundred thousand miles.
gpt
Is this a Great Crusade-era story? Because if so, the Astartes were only a part of the Imperial conquest machine. The Space Marines were accompanied by the Imperial Army (combined navy and ground forces) who did most of the occupying.

More generally, compliance doesn't require  permanent occupation. The Imperium, both Crusade and post-Heresy, prefers to leave as much of the existing power structure in place as possible during planetary conquest. Smashing governments to pieces and rebuilding them from scratch is an expensive ordeal at best and turns into a quagmire at worst. Regime change is rarely necessary, and complete overthrow even less so. A common tactic is to back any pro-Imperial factions and let them take charge. You don't have to take any land if you can get someone who's already taken it to side with you.

Establishing orbital superiority alone is often sufficient to force a surrender, since any resisting forces can be subjected to orbital bombardment with impunity. Any ground engagements (aside from those supporting general operations, like destroying strategic targets) are mostly to shock belligerents into realizing resisting is pointless or to obliterate any holdouts.