He was fucking back. He had ran away earlier to continue his vendetta with Homelander after realizing that everyone in The Boys were fugitives. This left you, M.M, Kimiko, Frenchie, and later on Hughie to get captured by some Vought commandos.

After breaking out, you guys took shelter in the basement of some antique store or something.

Now, Butcher was back. He was fucking back after being MIA for like 2 weeks.