Then to his amazement he realised that the room appeared to be empty. He and his wife looked under the desk, and behind the curtains, and even up the chimney. There wasn’t a sign of anybody. Yet the desk had been opened and the housekeeping money was missing.

     “Extraordinary affair!” the clergyman kept saying for the rest of the day.

     But it was not as extraordinary as the behaviour of Mrs Hall’s furniture a little later that morning.

     The landlord and his wife were up very early, and were surprised to see the scientist’s door wide open. Usually it was shut and locked, and he was furious if anyone entered his room. The opportunity seemed too good to be missed. They peeped round the door, saw nobody, and decided to investigate. The bedclothes were cold, showing that the scientist must have been up for some time; and stranger still, the clothes and bandages that he always wore were lying about the room.
Explanation:
 
To their surprise, the clergyman and his wife couldn't see anyone. The room appeared to be vacant. The clergyman and his wife looked under the desk. Then they looked behind the curtains and also up the chimney. But there was no sign of anyone standing in the room. They realised that the desk had been opened and the housekeeping money (the money used to buy food and other things necessary for living in a house) was gone.

After seeing the strange incident and the situation, the clergyman said, "Extraordinary affair". Here the term "extraordinary affair" means that something weird was happening around them. He used the phrase to describe what happened in his room. The money had been stolen, and no one could be found in the room. He continued to say such throughout the day since he was horrified by the occurrence. But what happened with Mrs Hall's furniture was far more interesting than them.

Mrs Hall and her husband woke up very early and were astounded as the door to the guest room was open. The door to the scientist room was usually kept closed and locked. If someone tried to enter his room, he would become enraged. Mrs Hall did not want to give up this chance. It might be because the scientist acted too strangely while he got inside the inn. Also, she knew that he was a scientist. So she could have wondered why this man was refusing to let anyone inside his room or why he did not want to talk to anyone else. So she had this notion about him, and she would believe it was better to examine his room when he wasn't in there.
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Opened room

Mr and Mrs Halls then decided to investigate when they saw that nobody was inside the room. His bedsheets were cold, indicating that he had been awake for some time, and all of the bandages he used to bind over his face were scattered throughout the room.
 
Meanings of the difficult words:
 
S.No Words                                            Meanings
 1CurtainA piece of material, especially cloth, that hangs across a window or opening to make a room or part of a room dark or private
 2ChimneyA hollow structure that allows the smoke from a fire inside a building to escape to the air outside
 3InvestigateTo examine a crime, problem, statement, etc. carefully, especially to discover the truth
 4PeepTo secretly look at something for a short time, usually through a hole
 5Opportunity A time or set of circumstances that makes it possible to do something
Reference:
National Council of Educational Research and Training (2007). Footprints without Feet - H.G. Wells(pp. 26-31). Published at the Publication Division by the Secretary, National Council of Educational Research and Training, Sri Aurobindo Marg, New Delhi.