Space Quest 4.5 and VSB offers a couple of alternative histories to outcome of the Aluminum Mallard after SQ4, than the one given in official Space Quest Companion.
Roger Wilco and the Voyage HomeEdit
In SQ4.5 game Roger returns to Magmetheus before the ship is impounded, and uses it to leave the planet, and ultimately uses it to get to the Starcon Academy.
After a few stops between Galaxy Galleria, Monolith Burger and Planet X, Roger returned to Estros. He was forced to leave the Mallard behind when Zondra forced him to go to the Wedding planet. Roger was able to jury rig his communicator in order to call A3D to bring the Alluminum Mallard and rescue him before he was married to Zondra. Roger jumped into hyperspace, but engines malfunctioned stranding him in space. After partially fixing the engines, he made his way to StarCon Academy. Engineers at the Academy fixed the Mallard in exchange for him finding a spy. After tracking down the spy Roger decided to join StarCon. Beginning his training he left the Mallard at the Academy.
Vohaul Strikes BackEdit
Later, the Alluminum Mallard is repaired (in both Paragon and Renegade endings) allowing Roger Wilco and Bea to leave the planet (either married and Bea with twins or relationship breaking down).
Incineratinos follows the renegade ending. But its not clear what happened to the Aluminum Mallard in the half-decade between VSB and Inc.
Following his adventure, Roger may have chosen to leave Aries 6, to travel where the stars would take him. He walked away from both Beatrice Wankmeister and Stellar Santiago. Aries Command gave him the refurbished Aluminum Mallard. He was happy, as he flew away from the station. Both Beatrice and Stellar looked up as he flew away, seemingly happy, that he was still free to travel the stars again.
Behind the scenesEdit
In official material, Roger Wilco lost the Aluminum Mallard while he was off in the future. It had been impounded for debts he accumulated over the course of his adventures. Roger was left with just enough money to book passage back to Xenon, where he joined the StarCon Academy.