Which is the correct way to punctuate the sentence? Dr. Burke wanted to trust her assistant with the secret formula; but she was afraid her assistant was a spy.
Dr. Burke wanted to trust her assistant, with the secret formula: but she was afraid her assistant was a spy.
Dr. Burke wanted to trust her assistant with the secret formula but, she was afraid her assistant was a spy.
Dr. Burke wanted to trust her assistant with the secret formula, but she was afraid her assistant was a spy.

i do not know what the passage is but i can give some examples

1. repetitive phrases may be used to create a emphasizing tone

2. pauses in sentences are used to create a dramatic effect but can also be suspenseful

3. using lots of exclamation marks and loud speech such as words in all caps can be creating a excited or possibly angry tone.

4. using lots of questioning phrases my mean that they are in suspicion of something.

5. using lots of questionable statements or questions can imply of a sneeky or sly tone.

he will find out what went wrong or happened and how.