A teenager who alleges a science teacher had sex with him in an an aeroplane toilet as they travelled home after a school trip has told a jury he felt lost and confused when she told him she was pregnant and was having an abortion.

The teenager, who was 16 at the time, wrote a note on his phone apparently addressed to Eleanor Wilson, saying: “Why are you doing this to me?”

Questioned at Bristol crown court over why he had written that Wilson had taken away his happiness and confidence, he said: “I was feeling emotionally lost, confused.”

Giving evidence from behind a screen, the alleged victim denied that the relationship with his science teacher, now 29, was a fantasy.

He insisted that a bond had developed between them during the trip and it was claimed she had given him her mobile number, which he had stored under the name “Smurfette”.

Wilson is accused of touching the boy during the flight before beckoning him into the toilet cubicle and performing a sex act on him. They then allegedly had sex in the cubicle.

The boy told the jury that during the trip in the summer of 2015 they sat together in the evenings and talked about their lives. He said he wanted to speak to someone in authority who could give him advice.

On the coach journey to the airport at the end of the trip, the teenager said he sat in the back seat with Wilson and other friends and her hand touched his. “It was not exciting, it was actually relatively strange because she was a teacher,” he said. “I removed my hand.”

He claimed teachers and students were drinking alcohol on the plane, and that he had drunk red wine and felt “reasonably intoxicated”.

Back home, the teenager said he bought Wilson chocolates and flowers and they visited the restaurant Nando’s. She gave him a lift home and he said he laid on his bed and they kissed and touched.

They visited Tintern Abbey and discussed future plans, he claimed. They also went to the Ashton Court estate, near Bristol. The teenager said Wilson encouraged him to break up with his girlfriend.

The alleged victim said he was in Wilson’s office at school when she told him she was pregnant with his child and planned to have an abortion.

Cross-examining him, the defence barrister Anna Midgley said it was not physically possible to perform the alleged sex acts within the confines of the toilet.

The jury was told another pupil tried to blackmail Wilson, telling her: “Reply in 24 hours or it [the rumours] will slip out. Wouldn’t want that would we? You know what I’m on about: you had sex with a pupil.”

The student added: “I’d love to do that – he’s very lucky. I’m a student with a big crush on you – I’m willing to hold back under one condition. The option is for you to have sex with me … Just think about it.”

The school principal, who cannot be named, said when she heard of the plane allegations Wilson told her she had no interaction with the 16-year-old outside school but later accepted she had taken him back to his home after the Nando’s trip. “She admitted that she had his number and he had hers,” the principal said.

Wilson, of Dursley, Gloucestershire, denies four charges of sexual activity with a child by a person in a position of trust.

The trial continues.