2 years ago NYC sewers

The turtles were on their way back home and decided to stop by the Alley and tell some of their friends about meeting Daredevil but before they got there they found Annalee of the Morlocks crawling toward them bleeding badly and heard screams echoing down the tunnels. They stopped and went to help her. She pointed Donatello tried to stop the bleeding but it was too late she died as a man holding a large gun came up. He chuckled, "You gonna run uglies?"

Raph looked at him with hate in his eyes and charged. The man called Scalphunter laughed at first and tried to shoot, Raph dodged and lept in the air. Scalphunter stopped laughing when the sai plunged into his chest, Raph yanked it out and kicked him to the side as he ran head on into the battle going on inside. Leo ordered Don to go get Splinter as he and Mikey followed Raph in.

The X-men had just arrived along with a few other teams and were fighting desperately to stop the slaughter when the turtles arrived. Cyclops looked at Raph running by and started to tell him to run but stopped when he saw him slam into Sabertooth hurling the villain to the ground. Sabertooth through him off but before he could pay him back the X-man Wolverine interrupted by slashing him across the chest. The Marauder Blockbuster snatch Raph up intending to crush his skull but the enraged turtle stabbed his sai into his eye socket killing him instantly.

Mikey and Leo went in more cautiously than their brother, Mikey went to help the injured escape while Leo yelled to the fleeing Morlocks, "Who among you is fit to fight?" A few dozen raised their hands," Come with me." The Marauders were shocked when many of the Morlocks fought back at the behest of the Turtle barking orders at them. Scalphunter started to get back up but Don and Splinter arrived, Don smashed his bo staff into his skull and picked up his gun.

They ran in and joined the battle saving many Morlocks in the process the battle had turned and the Marauders were beginning to fall back as Thor arrived causing them to flee like rats. Leo took charge of getting the injured to the makeshift hospital at the X-mansion while his brothers helped find the injured and other survivors that may have gotten lost in the mayhem. Callisto thanked Donatello saying if it weren't for the alarm system he set up they wouldn't have seen them coming and it could've been much worse.

The next day only a few of the Morlocks were unaccounted for. A few Morlocks had died but the battled ended worse for the Marauders who had lost most of their team. Many had been critically injured but were being tended to. The X-Men offered the turtles membership but they declined saying their place was with Splinter.

In the weeks that followed Donatello worked with Beast and the mutant Forge securing the Alley to prevent anything like this from happening again, the rest of the turtles along with several of the X-men and members of X-Factor trained some of the Morlocks into a makeshift police force.