Okay, I am gonna review the story of the entire 2012 origins before it takes place on Rise of the Turtles.
A very long time ago in Dimension X, Utroms had many personalities until one day, Kraang, a scientist Utrom discovered mutagen from a Kraathatrogon, a space worm. Since their sworn enemy, the Triceratons tried to wipe them out, Kraang mutated into a giant version of himself, giving himself the name Kraang Prime and brainwashed most of the Utrom into slaved copies of himself, the Kraang had been born and he even hired an Utrom named Knight who was remained Subprime. His ultimate goal is to find a new homeland which is Earth, which will mutate the entire world for their kind to live.
At the same time, there was a D'Hoonib humanoid named Professor Honeycutt who created a black hole generator, Subprime came over to buy the generator and he did. But however, Honeycutt is unaware of the Triceratons who wanted to use the black hole generator and wanted him to build a weapon. When he refused, the Triceratons attacked him and destroyed his lab. His robot assistant managed to save his life by transporting his consciousness and brain into the robot. Thus, he was given the name Fugitoid.
On earth, a couple named Hamato Yoshi and Tang Shen became parents to a newborn baby, Miwa. Shen suggested that they should move somewhere, like New York, which is in America, but Yoshi said that his father is becoming very ill and has to keep an eye on the dojo. However, Yoshi’s rival, Oroku Saki, who had been found as a child and raised as a Hamto warrior wanted Shen to be with him so he can raise Miwa. Telling Shen to take Miwa away, Yoshi started to battle Saki as the dojo started to engulf in flames. Fearing that her husband would be killed, Shen left Miwa on the bridge and cried to tell them to stop, but Saki accidentally killed Shen and died. Devastated, Saki runs toward Shen, but a burning debris causes him to become horribly disfigured. Finding Miwa on the bridge, Saki promised that he will take care of her, naming her Karai. Yoshi somehow was saved unharmed and rescued by unknown people (see Tale of the Yokai) and he was devastated that his wife and daughter are gone forever.
As Shredder rebuilt the Foot clan, he taught Karai that Yoshi “killed” her mother, poisoning her heart by the year. He started to recruit martial arts star Chris Bradford and South African criminal Xever Montes to do his bidding. He also works with an old friend, Ivan Steranko, who has known him for ten years.
Arriving in New York, Yoshi wandered around the city, still devastated by the loss of his family. Not wanting to be alone, he buyed four small turtles to keep him company. His attention was drawn to see a group of Kraang and tell him to go no further. Yoshi fought them and in a struggle, a mutagen canister fell on Yoshi and mutated him into a giant rat. The turtles that were touched by human hands also mutated into humanoid turtles. Realizing that the humans would fear them, Yoshi and the turtles retreat to the sewers, where he trained his four adapted sons to be ninjas. Thus, this began the series.