Did they inception him so hard they turned his real memories into a dream?
Yeah...in the end the alien doctor convinced him that the alien invasion was all a dream induced by some kind of machine. Meanwhile she also hypnotized him to make him think he still on Earth and he's living a normal life! Maybe it's better to believe in a lie, than knowing the sad truth.
It's interesting that this story share some similarities (the aliens who keep humans as pets) with "Oms en serie" (1957), which was later adapted into the animated movie "Fantastic Planet" in 1973. Maybe Ishinomori has read that novel, or maybe the concept of humans enslaved by aliens was common in the SF of the '50s and '60s, I'm not sure.