To perform surgery — literally to put a scalpel to (operate on someone/something).
担当医はすぐにメスを入れる決断をした。
The attending physician decided to operate immediately.
彼女は重傷で、救急でメスを入れられた。
She was seriously injured and underwent emergency surgery.
To take drastic measures or investigate thoroughly — figuratively to 'cut into' an organization or system to reform or scrutinize it.
会社の不正が発覚し、経営陣にメスを入れる必要が出てきた。
After the company's misconduct was uncovered, it became necessary to crack down on management.
市は教育制度にメスを入れるための専門チームを結成した。
The city formed a specialist team to overhaul the education system.
問題の原因を突き止めるために、第三者機関がメスを入れることになった。
To find the root cause, a third-party organization was brought in to investigate thoroughly.