The first order of business after securing the crime scene is securing the weapon as evidence, documenting the position where it was found, and searching the scene. While some investigators do this, others would be getting a detailed statement from the store clerk. Still other investigators would accompany the living suspect to the hospital, and after his treatment, have uniformed officers place him under arrest. Other uniformed officers can walk the crowd looking for anyone else who had seen what had happened, take their initial statements and contact information.
While observing the crime scene, the investigating officers need to locate and identify the position of the bat, and shell casings along with any other evidence relevant to the incident. The body of the victim should be photographed and its position noted carefully before its removal from the scene. An investigator ought to ask the store clerk if there is security footage of the store, and if so, investigators ought to take that in for viewing.
Later, investigators need to determine whether the clerk’s story is corroborated by other evidence, such as camera footage, positions of the artifacts (including the body of the DOA), and other witnesses. If the story of the clerk is corroborated, and the gun used for the shooting was legally obtained by the off-duty officer, then the shooting ought to be designated as justifiable, and the remaining suspect should be charged with aggravated robbery and assault/attempted murder of a law enforcement officer (if the officer identified himself as such).