Theory:

     Having finished his work, Ray stood up and was on his way to the back room when a cold rush of air from the front door hit the back of his neck.
 
     He turned to meet a last-minute shopper, but his old, wise eyes told him that this was not a shopper. He saw two men, one in his twenties, the other closer to fifty. The younger man remained at the door. The older man approached the counter with no sign of friendliness in his eyes. Ray was able to hide his growing fear as he slowly pushed a notepad and a pencil across the counter.
Explanation:
 
Having finished the work, Ray was all set to shut down the store. He stood up and was on his way to the backroom when the front door opened.
 
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Ray was on his way to the backroom when the front door opened

It should be remembered that Ray was a deaf man, and he didn't have the door in his sight when it opened. Moreover, since he was deaf, he couldn't have heard it getting opened or the noise that came from the outside. So how did he realise that he had a visitor?
 
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Ray was an old deaf man
 
So, when Ray had turned his back towards the front door, he felt a sudden rush of cold wind on the back of his neck.

Ray turned towards the front door, expecting to see a last-minute shopper. There were two men, one of them was about fifty years old, and the other man was in the twenties.
 
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Ray saw two men at the door
 
The younger man stood at the door while the older one approached Ray. The latter's look suggested that he didn't come to shop.
 
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The younger man remained at the door while the older man approached Ray

Ray was an old man and, hence, he was wise enough to see through people. When he saw the older man, he realised that the latter had a cruel look. His eyes lacked any sign of friendliness.
 
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The older man's eyes lacked any sign of friendliness

Ray started to feel scared, but he tried to hide them. He also decided to communicate with the man. Since it wasn't mentioned in the story that he was mute, it is possible that he could speak. However, he pushed his notepad and a pencil across the counter to communicate with his visitor.
 
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A notepad and pencil

Though the men’s intention was not expressed explicitly, it was suggested that they had come for money. The untimely hour when the incident was taking place, the older man's unfriendly look, Ray's intuition, the younger man at the door suggested that the men were there to steal. The latter's presence at the door indicates that he could be blocking the door, either to prevent Ray from running out or to block the shop's view from outside.
 
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The men have come to extort money from Ray
 
Meaning of difficult word:
 
Sl. No.
Words
Meanings
1
CounterA long flat-topped fitment or a table across which business is conducted in a shop
Reference:
National Council of Educational Research and Training (2006). The Old-Clock Shop (pp. 11-14). Published at the Publication Division by the Secretary, National Council of Educational Research and Training, Sri Aurobindo Marg, New Delhi.