You can create this with a switch, and a Conditional branch in the Event tabs.
First start off with creating the assasin event, and open up the event commands.
If you have a visible assasin, you can add a battle processing command first. If Its random you have to make the changes inside the troops section.
After adding the battle processing, select the command: control switches and name it to whatever you want (Asssasin Dead etc), and set the switch to be ON.
If you want your assasin to dissapear, but have the ability to come back after you exit the current map, you can add a erase event command after the switch. Or, if you want him to dissappear for good, you can use the self switch command. Set it to switch A and add another event page, then select "Self switch A is ON" to the left. Now when that event is done, we need to set the Npc that is blocking the way.
Just create your NPC as a new event.
Set the 1st page of the event tab, and open up the event commands:
Add a conditional branch and select the assasin switch as ON inside the branch.
Above the "Else" text, put in a Self-switch.
And under it put in whatever you want the Npc to say to your party, while the Assasin is still alive.
(or whatever you want him to do, leave it blank if you dont want him to do anything at all).
Add another page, and select the self switch to be ON. (Also make sure the next page doesnt have any graphics, this will make the NPC dissapear.)
Thats the way I usually do it, but you can skip the conditional branch and just trigger the Assasin Dead switch to ON.
There are of course other things you can edit, but thats a basic of it.
Hope it helped