Doom stood in front of a computer console in his lab, typing away at the keyboard. He was busy adjusting his information about the teen superhero. He thought about how one might defeat an individual who could become intangible at will.
"Knocking her unconscious could work." He thought out loud.
"What are you doing?" Shredder asked, walking into Doom's lab.
"Finding a solution to our problem." Doom replied.
Shredder glanced around the room, "What exactly is this place?"
"My lab. Don't touch anything."
Shredder narrowed his eyes towards Doom, "I've never been fond of scientists."
"I am no mere scientist. I am a scientific Genius and you will-" Doom was cut off by the sound of an alert. Doom brought up the monitor showing the location of the Doombots in Washington.
"What is it?" Shredder demanded.
"The Doombots have alerted me to unauthorized movement in that area." Doom told him, "There." He pointed to a section of the screen where a green helicopter appeared. It was shooting down several Doombots one at a time.
"That is unmistakably the turtles." The Shredder spoke, "Where are they headed?"
"Our direction." Doom replied.
"I'll send a team to intercept-"
"No." Doom interrupted, "Let them come. We'll be waiting."
"What of the girl and her powers?" Shredder asked.
"I have a plan to deal with her."

...

The teens were successful in escaping the Doombots and were now on their way to the castle.
"So, what's our first move when we get to Doom's castle?" Don asked.
"Doom could be keeping the FF on site. It may be faster to check the security room first." Mystery said.
"Careful, Leo," Mikey teased, "She might be taking your place as leader." He let out a chuckle.
"Now is not the time for jokes, Mikey." Leo told him.
"Stick in the mud." Came Mikey's mumbled response.
They flew through the skies, not making a sound. Finally they arrived at Doom's castle.
"Don't land too close," Leo warned, "We don't want him to spot us."
Don understood and landed the Shellicopter at quite a distance from the castle. They exited the chopper and headed towards Doom's home. They snuck inside, without realizing just how easily they did so. Making their way to the security room, they noticed the unusual lack of Doombots.
"Maybe they're all guarding the FF?" Mikey suggested.
They made it to the security room and found the door unlocked.
"Anyone else sensing a trap?" Leo asked.
The others nodded as they drew their weapons. Leo drew his swords and turned to face the other way; keeping an eye on what's behind them. Don slipped in first and went straight for the console. The others guarded his back; expecting anything. Suddenly the floor lit up with electricity. Leo, who was still just outside the doorway, spun around to see his team mate twitching from the electrical current being forced through their bodies.
"Arg,Run, bro!" Raph called, with what little strength he had left, "No point … in you getting' caught too." The electricity ceased and all but Leo fell to the floor unconscious. Leo leaned closer, making sure not to touch the floor of the room in case it became active again.
"Still breathing." He sighed with relief, and ran to the shadows to wait for Doom so he could follow. It didn't take Doom long to arrive, but what surprised Leo was that he was accompanied by the Shredder. Leo ducked further into the shadows.
"That worked better than expected." Leo heard Doom say.
"Not quite." Shredder told him, "There are only three turtles. One is missing."
"Curious." Doom inspected the room, "How did he manage to avoid the shock tiles?"
"That doesn't matter now." Shredder turned to his soldiers, "Foot ninja! Find him!"
They bowed quickly and went off in search of the last intruder, but Leo had managed to get inside an air vent and slip away unnoticed.

Doom ordered his Doombots to take the remaining teens to join the Fantastic Four. He stopped the one carrying Mystery briefly enough to place a breather over her mouth attached to a tank he placed on her chest.
"What is that?" Shredder asked, as Doom cuffed the girl's wrists and ankles.
"The gas will make sure she is too weak to use her powers," Doom replied, sending the Doombot on its way, "And the cuffs will keep her from removing it."
The Shredder nodded; impressed.
They followed the Doombots back to the Fantastic Four. They greeted Karai and Hun as they entered.
"Where's the fourth turtle?" Hun asked.
"Being dealt with." Shredder replied.
"Leonardo." Karai whispered to herself.
The Doombots restrained the turtles next to the Fantastic Four and Mystery across from the Thing.
"Strange." Reed inquired, "Why is she being kept separate?"
"Karai, Hun. Go help the Foot soldiers search for Leonardo." Shredder ordered. Without word or hesitation, the two left the room to join the ninja in their search.
"The circumstances are finally forming in our favour." Shredder said.
"Indeed." Doom agreed.