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The old man asked his lazy, good for nothing son to help him with converting the room, but he wouldn't, because he's lazy and good for nothing. Finally the old man had enough and decided to try doing it himself. He was doing quite well, managed to get the toilet out of the boxes and put it together, but when he tried to push it into place, the effort was too much and he died of a heart attack, falling face first onto the toilet. Then his good for nothing, lazy son came by, because he was feeling bad about being lazy and good for nothing. He found his father in the panic room, with his face in the toilet bowl, and didn't want his father to be remembered as someone who's died in such a ridiculous way. So he put him on the floor, shot him in the head with the gun he brought with him, got out and then called the police to report his father missing and start the search that would end in them finding the mysteriously dead (instead of ridiculously dead) old man in the panic room. Ta-daaaaaaaa!

The old man had a multiple personality disorder: one of the personalities had arthritis, while the other did not. The arthritis-less personality decided to get rid of the other one. Which makes one of his personalities the killer, and the other the victim.

The man was doing his bussiness in the room before he was killed. The killer put the gun next to his body to make it look like sucide. They locked it from the inside but managed to get out just before the door shut.

Maybe they are just filming a movie...?

I'm voting the murderer to be a remotely controlled robot (such as an anti-mine robot, with multi-functional 'hands').

The murderer is hiding out in a hole he made where the toilet is now sitting.

Maybe the wash-room is fake. Maybe the apparent pipe entrance is nothing of the sort; maybe they never intended to install the toilet, instead digging a tunnel to the vault of a nearby bank, the toilet being just a decoy... and then the old man walked in on the culprits.

The old man is a crazy scientist who managed to capture an alien shapeshifter visiting Earth. He locked it in an inescapable panic room. When the man came to study the shapeshifter, bringing the gun for safety, the being attacked him, shot him in the head and then turned into an inanimate object. It didn't know anything about Earth, so it shapeshifted into an only object it had available - a toilet that was packed in the boxes in the corner. Now it's waiting for the room to be opened, and once it is and there's no one around, the being is going to shift again into something that can move and escape.

lock himself in and bang his head on the toilet?

The killer used a laparoscopic tool snaked up the toilet line to shoot the man and put the gun in his hand.