Things are about to change big time for the family.
Agent Johnson was back in New York to try to find the pregnant turtle. Despite Agent Johnson's failures, Bishop had allowed him to have as many commandoes as he needed.
It had been well over three months since Leonardo had escaped from Agent Johnson's custody. The man knew that the turtle would head back to New York. He had found no signs of the turtle in Nebraska following the helicopter stealing. That turtle was a crafty one.
Johnson knew that he had to find Leonardo before it was time for the remaining two babies to be born. Agent Bishop needed the DNA from those valuable babies. And he knew the turtle wouldn't part with the babies so easily. He would find a way to subdue Leonardo and get the babies out of him when it was time.
…..
One night, a week before Thanksgiving, Don, Raph, and Mikey were out on patrol. It was a warmer night for once and they didn't have any clothes on other than their typical gear and weapons.
Seven commandoes were patrolling in a chopper and they spotted the three turtles on the rooftops.
"Agent Johnson, three of the turtles have been spotted."
Johnson perked up at that. "Pursue them, get a tracker on one of them. We might be able to find Leonardo that way."
"Yes, Sir."
The humans pursued the trio of turtles.
At one stop, Don saw they were being followed from the air. "Guys, I think we have trouble." He said, pointing.
"Bishop's helicopter! Don't let them shoot you! Run!" Raph ordered.
The three of them ran for their lives. Some darts and trackers in a rounder form were fired from the chopper.
The darts were not tranquilizers though. They were also trackers. They were meant to be distracters while the rounder trackers were to land on any one of the turtles' shells. But there were tranquilizer darts too, if they were needed.
The reptiles continued to get away. Then the order came to tranquilize them, then get a secure tracker on one turtle.
It didn't matter how much Don, Mike, and Raph tried to get away, darts were still fired at them, and they had gotten a few in their skin. They had only hurt them moments before, but now, darts were being fired again and this time, all three of them were hit in an arm or a leg and they began to get sleepy. But none would leave the others. In no time, all three were asleep on a roof.
The commandoes came down and checked out the turtles. Then one of them placed a secure tracker under the shell of Donatello, under one of his shell plates just next to the skin on his side. They were going to lead the humans to their lair whether they liked it or not, and Johnson was going to get his pregnant turtle back.
….
The turtles soon came to and found themselves still on the rooftop and found no humans around. They looked themselves over and saw the small wounds inflicted from the darts but there were none around. Otherwise, they were just fine.
"We have to get back underground and tell Leo that the commandoes were after us." Don said.
"No kiddin'. Let's go!" Raph said.
The commandoes were now out of the chopper and were following the signal. They made sure that they kept a distance.
The turtle brothers got down from the rooftops and got into the sewers again.
The commandoes waited a little bit, and then followed them down and toward their lair no doubt. They called in double reinforcements.
…
When they finally came back to the lair, they immediately spilled the beans to Leo and Splinter, who had been meditating together.
"You don't think they're trying to find Leo, do ya?" Mikey asked.
"I'm sure that's exactly what they're doin'." Raph said.
"But they didn't take any of us this time."
"There must be something else at work if they didn't take any of you." Leo said.
Then, all of a sudden, noises started coming from outside the lair that sounded like blasting. All of the turtles and Splinter stood up, taking out their weapons.
"What's going on?" Mikey asked nervously.
"I don't know." Don said.
"We're about to find out." Leo said. Even he had his katanas ready.
"Stay behind us, Leonardo." Splinter said.
Leo wanted to lead the attack, but knew that he had to stay back.
The wall near the satellite television monitors exploded and several commandoes came storming in.
"Commandoes!"
"How did they find us?" Don exclaimed.
"Doesn't matter how! Now to kick some butt." Raph said.
The family attacked except for Leo and Don. Don stayed near Leo to protect him.
"Give us the blue masked one and we may let you live." A commando was talking.
"Never! You will not have my son again!" Splinter growled and hit the commando's gun away and hit him in the stomach and the head.
Raph and Mikey had fun hitting and knocking out many commandoes.
Then, some giant footsteps could be heard. The attack stopped. And the same wall got a bigger explosion and in wheeled some giant tanks.
"No!" Leo whispered.
"Stay behind me, Leo." Don said.
"Turtles! So good to see you all again. Ah, and Leonardo! Just the one I wanted to see." It was the voice of Agent Johnson. "Nice home, mutants, but now, it's over!"
"You ain't never gettin' my brother again!" Raph yelled.
"We'll see, Red." Johnson said.
Leo kept his stomach hidden behind Don's back.
Many more commandoes came in and attacked. The Turtles and Splinter were fighting the hardest that they could. But eventually, Don got pulled away from Leo and Leo was surrounded.
The humans could see Leo's delicate condition and the pregnant turtle had a hand on his stomach and a sword in the other hand.
"Leave me alone!" Leo warned.
But the men came in anyway, in an attempt to corral Leo.
"Don!" Leo cried out.
"Leo!" Don heard Leo's cry for help, but was too busy locked in combat, and was hit in the face and knocked down. And the tracker slipped out of Don's shell.
Leo still remembered his old ways of fighting. He cut up the guns. He hated to jump about, but it was leaving him no choice. But then, he saw Mikey was closer to him now and he saw he was in trouble.
There were some humans in here that were martial artists too and they were no trouble to take out, but Mikey was overwhelmed.
Leo jumped across one of the walkways. The landing hurt, and made him pause for a moment.
"Get back here, Turtle!"
Leo ignored the one who had been after him and continued over to Mikey. He also noticed something else, one of the machines was aiming at Mikey.
"Mikey, move!" Leo shouted to his baby brother.
There was a blast and Leo shoved Mikey out of the way as the blast traveled overhead and blasted into the room that headed into Don's lab.
Mikey landed safely, but Leo was flung hard into a wall and debris fell from the ceiling.
Leo saw it coming and knew he couldn't move fast enough. He quickly protected his head. He just hoped his babies would be alright.
Most of the debris landed close to Leo, but a good deal of small stuff landed all around him until he was buried.
"NO!" Don cried out. He saw Leo's predicament and his lab was most likely ruined now, including the incubators.
Raph was closer to Leo. He went over to get Leo out of the debris.
The place was beginning to cave in.
"Don, get Mikey and get out of here! Splinter, go, I'll get Leo!" Raph ordered.
The orders were followed. They could no longer stay here.
"No you don't, Turtles!" Johnson said.
Commandoes were still around and were firing. The shots were only for stunning.
Raph got to Leo and dug him out. "You ok, Bro?"
"I think so." Leo said.
"Good. Come on. We have to go." Raph helped Leo to his feet and they went out another way and into the sewers. They would go to April's.
"You fools! You were not to harm the turtle I wanted!" Johnson snapped. "Now he's gone again! Find him!"
Commandoes followed the trail, but all the smoke made them lose Leo and Raph's trail. But they went different ways to try to find them.
The two of them had hidden in a nearby tunnel.
Leo was in an incredible amount of pain. He was no longer used to all of that activity. Raph was keeping close to him. "You sure you're ok?"
"My stomach just hurts, Raph. I need to sit down." Leo said.
Raph had Leo's arm over his shoulder. He slipped it off and let Leo sit down. "Ok, just relax, Bro. I'll get ya out of here." Raph then went to check the perimeter.
Leo couldn't believe this was happening. He and his family had just lost another home! And he was right at the beginning of his third trimester! They had nothing left!
Mikey had found his cat, but he and Don were struggling to get away from the commandoes. They would attempt to lose the humans and then go to April's or Leatherhead's. They just hoped Leo and Raph were ok. They had seen Splinter get out and were sure he was fine.
When Mikey and Don were further away from the lair, they bumped into Splinter.
"Are you two alright?" Splinter asked.
"Well enough, just covered in dart cuts and bruises from the fight." Don said.
"Have you seen Raphael and Leonardo?"
"No, Sensei. We were hoping they were with you." Mikey said.
"And Leo needs to be scanned as soon as possible to make sure this didn't harm the babies." Don said.
"Yes. Another reason to find them." Splinter said.
They went looking for the others, but had to still fight off many commandoes. This was going to be another hard time in their lives with no home to go back to.
Beta read by Applepye.
Just to make it clear, through this whole story, the family had been living in the lair that was beneath Central Park. And just to add that the Fast Forward season never happened in this story. And yes, I do have them find a new lair too before the story ends. But its a surprise where they go to live.