How to use 'Nisei MK II' free 'End the run'?

Question

From the 'Nisei MK II' card:

Place 1 agenda counter on Nisei MK II when you score it.

Hosted agenda counter: End the run.

Does this really means that you get a free 'End the run' that the corporation can use a any time?

Answer 1

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)

Answer 2

user1873's answer is correct. To clarify further, the Corp will probably choose to use Nisei's ability at phase 4.3 of the "Timing Structure of a Run" diagram located in the FAQ. After the Runner has bypassed the final piece of ice, approached the server, and decided whether to jack out or continue the run, but before the run is considered successful, there is one final chance to use paid abilities such as Nisei's. It is during this final chance that you will use Nisei's ability.

If your intuition is telling you that this is a powerful ability, your intuition is right. There is some BGG discussion here. 4 cost for 2 agenda points is a bit on the steep side, but the ability is extraordinarily powerful.