Alex's body was found on Waitarere Beach, near Levin, on October 8 after his disappearance sparked a huge manhunt.
During the search, police released CCTV footage showing Alex and McIsaac together in a local store on October 5.
Court documents show Alex was allegedly murdered by McIsaac either that night or the next day.
McIsaac is also charged with unlawful possession of a knife in a public place and burglary.
The burglary charge alleges McIsaac unlawfully entered a property on Park Ave, Waitarere Beach, between late September and early October.
He is yet to enter pleas to any of those or a fourth charge, which is suppressed.
McIsaac was ordered to stay in custody until late April.