How to get Capacitors
Capacitors are the Den's second currency. Credits buy most of an upgrade, and the ones that change how the squad fights want Capacitors on top, which is why the ladder stalls on them rather than on money. They come from two places and there is no shop that sells them.
The short answer
Run missions and take the operations that pay them. A mission's bonus reward is one weighted roll, and Capacitors are 10.8% of it: 8.3% for a small batch and 2.6% for a medium one. That is the steady supply, and it arrives whether or not you ask for it.
The rest come off operations. 14 pay Capacitors on one of their options, and the option is the whole of it: the batch sits on one branch and the others pay credits or influence instead. Nothing in the Black Market sells them, no talent produces them, and no mission pays a fixed batch.
What they are for: 34 Den upgrades ask for Capacitors on top of their credit price, and three operations charge them as a cost. The upgrades are the ones that add a mod slot, a utility slot, a roster place or a point of Advantage, which is why the ladder tends to stall on Capacitors while credits pile up. Credit prices are on how to earn credits.
Not the same thing: the blaster mods
Four Power Cell mods carry Capacitor in the name and are unrelated to the resource. They fit a blaster, not the Den, and they are bought or rolled like any other mod.
Operations that pay them
The option named beside each one is the branch the Capacitors sit on. Where the asset states a number it is here; where it does not, the game shows the batch when the option resolves.
Den upgrades that ask for them
The credit price is beside each one. Where the asset states how many Capacitors it wants the number is here; the rest ask for a batch the upgrade screen names.