Kalil can be found where P-33 is, at the last room of the Junk Heap during the second Act of NieR Replicant.
Kalil is the little Shade that can be seen sitting atop the defense robot, P-33, during battle. They believed that the Shade was controlling the robot, but instead, Kalil and P-33 had actually formed an unlikely friendship and the robot committed himself to defending the little Shade from humans.
Kalil lost his mother Shade to humans and was found crying by P-33, who discontinued his intruder protocol when he received an error seeing Kalil crying. When P-33 decides to dedicate his defense system to protect Kalil instead, they become inseparable. Kalil spends his time teaching P-33 about the outside world in hopes they would someday leave the Junk Heap and explore the outside together.
Kalil is only seen atop P-33 during their boss fight sequence until his backstory is unlocked during the second playthrough.