In a story, which of the following is correct?
He thought that it is going to rain.
He thought that it was going to rain.
He wondered if it is going to rain.
He wondered if it was going to rain.
The reason why I am confused is that the characters would speak in present tense in a story. For example:
“It is going to rain,” he said.
I’m not sure but aren’t ‘thought’ and ‘wondered’ past tense?
If you’re having a thought in the present, aren’t you thinking?
He thinks that it is going to rain.
He wonders if it will rain.
Yes, but only if you’re writing the entire thing in the present tense (Harry was walking towards the door. Harry was answering the door. Harry was opening the door). Generally you’re not saying what’s happening, but reporting what’s happened after the fact (Harry walked towards the door, answered it, opened it). It all depends on how you’re writing it; it should fit in the same tense as the rest of the text.
As for your two example, the second in each case is correct; you’re putting the action (wondering, thinking) in the past tense, so the rest of the sentence should conform. So it would have to be either;
He thinks it is going to rain.
He thought that it was going to rain.
The latter is correct for both of your pairs. You aren’t quoting his thoughts in your sentence, so it’s appropriate to remain in the past tense. If you were to quote his thought, you would write “He thought ‘It is going to rain.’”
The trouble is that some of the most famous books and best writers will often mix tenses and perspectives.
Although any writing teach will insist you keep either the viewpoint of one individual, or else the omniscient perspective, it’s simply hard for even the best writers to write that way. They can’t see that they have shifted for one scene or two because they are so close to it, and orignially had a choice of several tenses or perspectives. The more famous they are the less an editor dares to object.
This example is not present tense, it’s some form of past tense (can’t remember what it’s called) because you are describing an ongoing action which occurred in the past. Present tense would be, “Harry walks towards the door. Harry answers the door. Harry opens the door.” Oddly, you rarely find the present tense used except in newspaper headlines or as a device to create tension (aren’t you expecting some horrible fate awaiting Henry on the other side of the door?).
Wow, that was fast. 
Thank you so much for your help!
It’s just that when one think about a person in the past tense. It sounds like the person was dead already…
Looking back on it, you’re right. :smack: Sorry, Vct1, but I think the rest of my post still stands up.
Don’t worry about it at all. It was very nice for you to help.