Side mission 1
You have to burn the poisoned blankets. Defeat the guard beside them and press the interaction button.
Side mission 2
Take the diseased to the clinic so that they can get a vaccine. You need to approach them and press the interaction button to take them to the designated spot.
The mission will end when you put the diseased onto the beddings.
Side mission 3
Kill the poisoned dog.
You will have to protect a square with the diseased from waves of Templars. Enemies will attack in accordance with the timer at the top of the screen. The first group will approach you from the north, the second from the east and the third once again from the north.
To defend yourself, open the Assassins Guild menu and choose "Ambush" by the clinic exit right before the timer hits zero. Your recruits will then attack any enemy who runs into the marked area.
Apart from that, use the pistol to shoot barrels on the ground. Their explosions should cause serious damage to enemy forces. With the last group eliminated, the mission will end.