It all began during the time when Donatello was infected with the outbreak virus. One of Agent Bishop's scientists was intrigued with these mutant turtles. He had just been hired not too long ago for the research that Bishop did in his hidden government headquarters. He had barely gotten to see the monster turtle turned back to normal before the mutant family ran out of the building before it was going to be destroyed.

Though this scientist was intrigued with them all, the one that he found the most fascinating was the blue masked turtle. He had such a caring and grownup maturity to him. He found his name was Leonardo. But he also wanted a chance to see the monster turtle turned back to normal too.

After the turtles had gotten away when Donatello had been turned normal again, it was several weeks later when he saw the turtles next, during the battle of New York, trying to protect it from a demon. But now that that battle was over, it was time to set his plan into action.

This man had enough experience in the fields of science, biology, math, medicine, and business. He wanted to start a project of his own, and Bishop would grant him this, as long as it was beneficial to their work.

The man said he wanted to study and work on the mutant turtles.

Bishop wasn't too surprised. The turtles were certainly worth studying. They were the only ones of their kind.

The man didn't want to kill the turtles, but when the ones he wanted were captured, he would go to any lengths to keep them restrained and contained until he could get what he wanted. And he had a special idea of how to get something from the turtles that would aid in their work.

The first one that the man wanted was the turtle that had been turned into a monster: Donatello. He wanted to see what he could do. He had heard that he was the smart one, so he had to be worth something.

Commandoes went around different parts of the city at night, looking for the turtles on patrol. They knew they mainly came out at night. They would get the purple masked turtle even if he was found with his brothers. But the orders were to tranquilize any others with him and just take him alone.

One night at Smitty's junkyard, which was Don's favorite one, Don and his brother, Raphael, the red masked one, were salvaging parts to upgrade the Shell Cycle. Don had his duffel bag to collect the supplies.

Raph wasn't too pleased about being there, but he wanted to get away from Mikey annoying him tonight. And he knew what few parts for the Shell Cycle might need. He was a little tech savvy like Don when it came to his bike.

The commandoes snuck in and got the two turtles' attention. Their guns were on stun, but there were also men with tranquilizers ready. A transport truck had been called before they had engaged. They were confident that they would achieve their goal.

Don and Raph stopped what they were doing and withdrew their weapons. Standing back to back, they did their bast to deflect the shots.

"Raph, we have to get out of here!" Don shouted over his shoulder.

"These are Bishop's flunky commandoes!" Raph said.

"Another reason to find a way back to the sewers." Don said.

"You go first. I'll cover you." Raph said… Then everything went black.

Raphael was awoken by the sounds of his shell cell going off. Rubbing his head, he looked around and gasped when he realized what had happened. "Donny!" He shouted into the night as he looked around for his brother. He then answered his phone.

"Hello!" Raph said groggily.

"Raph! Where are you and Don? It's 3 in the morning!" Leo's angry voice sounded on the line.

"Leo! We were ambushed by commandoes! We were knocked out and it looks like they took Don!"

"What?! Where are you?" Leo demanded.

"Smitty's Junkyard."

"We'll be right there." Leo said and hung up.

Raph continued to get his bearings and he collected the duffel bag and Don's bo and phone.

It didn't take long for the Battle Shell to pull in. Once Leo and Mikey got out of the truck they began to look for clues.

"Why would they want to take Donny?" Mikey asked.

"They never said, but it can't be good." Raph said, his head still screaming from the tranquilizers. He already felt a guilty conscious because he couldn't protect his brother, but he would make it up to Don when they found him.

Beta read with Applepye.