You make two scarves and join them with the hood stitches. Those are the 48 stitches that you'll cast on to join them. 26 + 48 + 26 = 100 stitches total.
With any pattern that looks complicated, I suggest that you just forge on, line by line. Don't look too far ahead. It's kind of like looking at page 8 of the directions for building a bicycle. "Fit flange B into slot C."--until you have flange B and slot C in front of you, it makes no sense. Very often with knitting, until you have the piece in front of you, it's impossible to visualize how it will all come together.