I don't have an exact episode number... but it 
might be from the following episodes:

The episode where Nuriko tells Miaka she lost an 
important jewel (or something...it's been awhile) 
and Miaka goes down to the lake and thinks she's 
attacked by a monster that turns out to be a 
log...

Or...

The episode where the undead attack the group in 
the forest.  Is that when Tasuki shows up?  

Those are the two scenes with "darker tones" that 
first pop to mind.  ^_^;

Again... it's been a LONG time for me... x_X