'Actually' and 'in fact' are usually used to state that what immediately follows or preceeds it is true.
It is used often in answer to a statement to say that the original statement was not really true.
"Are you a junior at the university?" "Actually, I'm a senior."
"Did you go to China." "In fact, we visited three other countries besides China."
"People think that he is great. Actually, I think he's a complete jerk."
'Indeed' is used to emphasize a point as being true; also it is used to express surprise.
"This is indeed a great occasion!"
"We just got married." "Indeed! I hadn't heard about it."