To make your way to Shiva for the final confrontation with her, you will need to jump through some hoops first.
In the middle of the Bowery, you will be able to hear a baby crying, a sound that will be coming from a baby carriage in the lower section of the area under the glass canopy. Once you investigate, you will then have a talk with Shiva and she will tell you there is a man in trouble somewhere.
To find him, go to the map marker and enter the mall there. Rescue him by destroying the electrical panels on each upper story to the left and right and fighting off the ninjas that appear. Once the guard is free, you will need to use your fancy gadgets to track the blood trail left behind.
As you reach the end of the trail, you will need to talk to Shiva one more time and then finally make your way to Sheldon Park to enter the Wonder Tower. Once you enter, Shiva will exit the elevator. Now it's time to get down to business.
When the battle starts, there will be plenty of other enemies with swords so I hope your knife dodging is up to snuff. Counter and dodge all the sword attacks as they come at you and quickly try to aim only for Shiva. Many times while you go right for her, the other enemies will stand around or just one will attack you. Counter that attack and continue to focus on Shiva.
Once she is down to half health, three martial artists will appear to fight. Depending on your knife dodging skills, these can be much easier to deal with. Again, just mainly focus on Shiva, countering the others when needed, but once Shiva reaches almost zero health, the other enemies will disappear and the fight will be over.
For more tactics here's our full Batman: Arkham Origins boss guide!