How to use 'Nisei MK II' free 'End the run'?
Yes, you get one 'End the Run' ability, because the card has one hosted agenda counter. From the rule book

Cards can also host counters and tokens. Hosted counters or tokens can be spent, or leave play, without affecting their host. If a trigger cost requires one or more hosted counters, those counters must be spent (retuened to the token bank) from the card that the ability appears on. (page 22)
Paid Abilities - Some card abilities have trigger costs that a player must pay before the effect of the ability can be resolved. These abilities are called paid abilities. A card’s trigger cost is always listed in its text box before the effect, following the format “cost: effect.” (page 11, sidebar)