We come back right after the general ordered the army to bomb the city. The GCPD is taking in all the refugees that are coming from all over the city. After Nyssa awaited Barbara and the baby in The Sirens club, she has taken them back to the City Hall. Nyssa wants to destroy the city before she will allow Barbara to die and she wants to keep the baby and raise her as her own. At the GCPD they have discovered that nobody can reach Barbara and Lee so Selina goes to The Sirens club to check it out.
At the docks, Penguin and Nygma are ready to leave Gotham, but before they can leave Penguin starts to doubt his decisions. The city is part of him and he can’t leave and watch it being destroyed. Nygma tries to persuade Penguin by saying that following his heart never worked out for him, but Penguin has made up his mind. He leaves Edward the dog with Nygma and goes to the GCPD. There he offers his help to Gordon just as Bullock comes to tell that Bane broke through the barricades. Then Nygma also arrives at the GCPD to offer his help. His excuse is that the submarine takes two people to work, but he also cares about this city as much as Penguin does. The entire GCPD stands together on top of the barricades to have a fire off between them and Bane with his soldiers. One of Bane’s soldiers throws a grenade onto the barricade and when Penguin tries to protect Nygma from the grenade, he is hit in his eye. When Bane uses a missile launcher to blow a hole in the barricades, the GCPD has no other choice but to retreat.
Meanwhile, Selina finds an unconscious Lee in The Sirens Club. She tells that Barbara is taken by Nyssa and together they watch The Narrows being destroyed by the army before heading back to the GCPD. They let Fox know what is going on and he gives the news to Gordon, with the information that the signal of the Generals brain chip also comes from the City Hall. Gordon makes up the idea that he needs to go to the City Hall alone and fry the General’s brain chip so that he can reverse the bombing order.
But this takes some time, so the rest needs to come up with a way to slow Bane’s army down. Bruce has the idea to turn Jeremiah’s old bomb -that is now a power source- back into a bomb and use part of Jeremiah’s maze plan to slow the soldiers down. But for it to work, he has to blow up the Wayne Enterprise building. He seems to not have any doubts so Selina joins him. When they arrive at the Wayne Enterprise building, the best place for the bomb is underneath a portrait of his parents. Bruce claims that his parents literally gave everything for this city, so now he has to do the same. They plant the bomb and the building falls on top of the soldiers.
Gordon has arrived at the City Hall where he defeats the guards guarding Barbara and frees her. But before they can free their baby and get out of there, they are surrounded by more men and Nyssa with their baby. Nyssa hands over the baby to the General and her and Gordon start to fight. When Nyssa is distracted, Gordon uses Barbara’s handcuffs to chain himself and Nyssa together. Barbara finds a gun and kills all of Nyssa’s men before she and Gordon work together to stab Nyssa with the same knife as killed her father. Nyssa lets the General execute the failsafe, which is shooting himself through the head. After this, Barbara gets the baby and Gordon holds his daughter for the first time. Nyssa escapes and makes it to the docks where the submarine is located and escapes with Edward the dog.
When Bruce and Selina walk back to the GCPD after they destroyed Wayne Manor, they are stopped by Bane. Both Bruce and Selina starts to fight with him, but Bane captures Selina and is willing to kill her. Selina can reach her knife and stabs Bane and frees herself. Then Bruce plants one of Fox’s devices on Bane that has some glitches. It attracts bats and Bane is attacked by them. Bruce and Selina escape and Bane rejoins his soldiers after he got rid of the bats. He and his soldiers move further to the GCPD where they surround the building. Gordon orders Lee to take Barbara, the baby and all the refugees to the tunnels laying underneath the GCPD. These tunnels should take them into the subway lines where they can get behind enemy lines and be safe.
But Lee has other plans and leaves Barbara and the refugees to stand by Gordon and the rest to stop Bane. Bane calls it a firing squad. But before Bane’s soldiers can shoot them all, Barbara and all the refugees come back and stand behind Gordon and the rest. This causes some friction between Bane and the soldiers because they are not ready to shoot and kill all those innocent people. Gordon gives the soldiers the option to either stand with Bane or with him and all the soldiers then point their guns at Bane and he is captured.
After Gordon contacts the mainland and explains what happened, the soldiers are instructed with a new task of rebuilding Gotham. When Barbara and Gordon finds a moment alone, Barbara reveals their daughter’s name: Barbara Lee Gordon, to the two women who always be there for her. Meanwhile, Penguin and Nygma make a pact together to rule the city again. Both of them are thinking about betraying and stabbing each other, but then they decide that neither of them can hurt the other.
Sometime later, we see the ceremony where Gordon is now promoted to commissioner. At the party, he meets Bruce who tells him that his life in Gotham is becoming too public and therefore he will go somewhere else. Alfred recovered reasonably from his encounter with Bane and walks now with a stick. He will oversee the rebuilt of the Wayne emperium when Bruce is away and waves him goodbye at the airport. When Selina arrives at the GCPD to find Bruce, she is handed a note from Harper but when Selina arrives at the airport she sees that she is too late to wave Bruce goodbye.