HOML (TMNT 2012 version x TLH Crossover)

Shredder's life was nearing its end, his body grew weaker every day, so his scientist Baxter Stockman suggests Genetic Cloning, but a quick scan reveals Shredder has been exposed to so much Mutagen gasses that Genetically Cloning him would impossible, unless they used a person and overwrite their DNA and rewrite their mindset. But the person needed to be young, have a congenital disorder[a medical condition that is present at or before birth.], and needed to have gone through several chemical exposures.

Only one person fits these criteria, Lincoln Loud, so Rahzar, Tigerclaw, and Fishface raid the Loud House, killing Lynn Sr, and seemingly killing the rest, but not really, then leaving a Mutagen bomb to put the blame on the Krang. While Lincoln was turned into a new Shredder, Rita and the Loud Sisters were turned into mutated Monsters.