Deep in the sewer Mikey, Ralph, and Donnie mourn the loss of their brother Leo. While fighting their last battle against Master Splinter Leo was killed. After talking it over they decided that they were going to get some food to try and settle their minds. Mikey suggested pizza so they ordered three. When the pizzas arrived Ralph and Donnie thought they looked a little weird. All Mikey could think about was eating so he took a bite of the pizza. Little did he know the pizza was a poison pizza, and it was going to kill him as well. Before he could take another bite he bent over holding his stomach. Before any of them knew it Mikey dropped to the ground and was pronounced dead by his brothers.
So upset with the deaths of their brothers Ralph and Donnie took off from the sewer headed for New York City. When they reached it they noticed the people walking slowly with far away looks in their eyes. One of the people walked up to a dog going across the street and attacked it. Before they could do anything UFO's showed up and started killing the creatures the humans turned into. Donnie was about to go and fight the aliens but Ralph grabbed him by the arm and took him back into the sewer.
Not happy Donnie tried to go back and fight but Ralph told him that he already lost two brother and he didn't plan in losing another. They decided that they were going to try and make an antidote for humans. They slaved away for hours and hours until they came up with what they hoped could cure the humans. As they walked back to the surface they decided that they were going to inject every human they could with the antidote and fight as hard as they could to save the world. As soon as Donnie stepped onto the sidewalk he was bitten hard on the arm. His body began to shake as he fell on the ground. With a face full of horror Ralph injected Donnie with the antidote. When Donnie came to he jumped to his feet and they began to fight off the aliens and give the people the cure.
After the aliens started to fly away the humans noticed the two huge turtles and they began to panic. A near by police officer took out his stun gun and shot both Ralph and Donnie in the legs. Calling for back up the officer began to drag both turtles into the back of the police car. When they made it to the jail house all of the police men surrounded the turtles and took them towards the jail cell. Being a rebel Ralph began to fight off the police men until he was tased agan and was thrown into the cell next to Donnie's.
One of the police men decided that he was going to take both of the mutants and put them in different states so that they could be found by the secret service men he had called. Since Ralph was still out cold he put him in the back of his car and drove for several hour before he reached Mexico. He dumped Ralph on the side walk and took off. When Ralph came to he dragged himself into a near by ally. Back at the jail house Donnie turned on his T phone that the police didn't know they had and set the tracker for Ralph's phone location. Donnie noticed the guards coming towards his cell so he sat and waited. When they opened the gate Donnie attacked them and escaped.
As he ran away from the Police station he looked at his T phone and began to follow the red dot that led to Ralph's T phone. After searching for 7 hours Donnie finally came across Ralph who was hiding in an ally way in Mexico. After Ralph was found everything began to become unfocused. Shoting up right in his shell Ralph noticed that he was back in the sewers under New York city. Ralph looked around and saw all of his brother laying down snoring and sleeping piece fully. That's when he realized that everything had been a dream.