Some TMNT stuff really isn't for little kids.
When April O'Neil first took Splinter, the Turtles and the human Casey Jones to her family's farm after their retreat from New York City at the end of the preceding City Fall story arc, she let Splinter and the Turtles stay in the barn, considering that April's parents John O'Neil and Elizabeth O'Neil were still living in the farmhouse and didn't know about April's mutant friends. During their stay, the mutants slept out of view in the barn's hayloft.
In issue #31: Northampton, part 3, the Shredder's new mutant subordinate Koya, accompanied by Foot Assassins, had tracked the Turtles, Splinter and the since-arrived Alopex to the farm, ambushing the group by piercing a hole in the barn's roof. The battle continued into issue #32: Northampton, part 4, and the barn door was completed destroyed by a Foot grenade. Leonardo achieved a temporary victory by puncturing Koya's aorta, causing her to bleed rapidly from her neck and forcing her to retreat to save her own life. But as the farm was no longer safe from Foot Clan, the Turtles left the barn they had been living in and returned with April and Casey to New York.
The barn reappeared in Teenage Mutant Ninja Turtles Universe issue #9: Toad Baron's Ball, part 1, when Alopex and Angel Bridge were visiting the farm and Angel was using tools in the barn to perform maintenance on Nobody's Exo-Suit. The barn took on a different appearance in this story, with a taller silo adjacent to the structure.
The barn reappeared again in the Leonardo macro-series issue, when the four Turtles were visiting the farm by themselves. The barn appeared more as it did during the Northampton story arc, and the damage inflicted during the fight with Koya and the Foot Assassins was still visible in the structure, having never been repaired.