Leave the museum and head NE. You're aiming for just south of Park Row and the Ace Chairman's Building. You could also just follow the blood trail there but hopefully this will save time. On top of the NE corner of this building, you should find bandages. Scan them when prompted and then chase after the Ninja. You will follow her for a little bit and then catch up to her. When the fight starts, just wait for her to attack you and then counter to plant the tracker on her. Meet a friend and act like a jerk.
You are tracking the assassin again but this time you will be quite a ways away. Follow the arrow and the box to your destination which should bring you all the way around the city to the Southwest part of the Industrial district. You'll find a Subway Maintenance Access that you want to jump down. It might be best if you try and glide and then dive bomb down because there are a few guards around the top with guns.
