Upon arrival in the Heleus Cluster, the Natanus struck the Scourge, causing massive damage to the ship and multiple casualties among the turian occupants. Macen died while attempting to transfer his SAM to his second-in-command, ex-Spectre and security officer Avitus Rix.
Because of this, the transfer failed and corrupted the AI's processes. It tried everything it could to comply with Macen's last orders to reach Avitus and get the ark to its destination, including ejecting stasis pods and going through the Scourge regardless of ship damage.
Mass Effect: Andromeda Edit
If Pathfinder Ryder accompanies Avitus to the last known location of Natanus at Remav, Macen's audio logs aboard the crippled vessel tell what happened. One of his last wishes is for Avitus to receive the Pathfinder mantle, which he may or may not accept depending on Ryder's suggestion.