you go to Linus's house and get the pen off his desk
You get it from Linus by giving him the sucker.
It is on the table after you give Linus the lemon sucker from Pigpen. Linus gives you his invitation to the Halloween Party, and he has just written a letter to the Great Pumpkin. Pick up the pen.
You give it to Charlie Brown, and he will sign Lucy's contract
When you give him the lemon sucker from Pigpen. He gives you his invitation to the party, and you can get his pen from the desk.
AT PEN ISLAND
After you get the invitation and the pen, Charlie Brown and Snoopy are in his backyard, on the far left of the island. You will play a mini-game as Snoopy gathers some leaves in a very relaxed manner.
You can find the pen after you give Linus's candy bag to Pigpen, who is on the street. In return, he will give you a lemon-flavored sucker. Then go back into the house and give it to Linus, who gives you his party invitation. Pick up the pen, which he was using to write a letter to the Great Pumpkin.
The pen, which you need to do the Charlie Brown football scene, is on Linus's desk in Linus and Lucy's house. It will appear when Linus is writing his letter to the Great Pumpkin. This is after you have selected the pumpkin in the pumpkin patch and rolled it back to the house. Take the bag that Linus gives you and give it to Pigpen on the sidewalk outside. He will give you a lemon sucker. When you take this back inside and give it to Linus, he gives you his invitation to the Halloween party, and the pen is on his desk. Linus is writing a letter to the Great Pumpkin.
You get the pen on the table
The pumpkin patch is to the right on Great Pumpkin Island. It was the only area shown in the island preview.
After you take the bag to Pigpen, and bring back the lemon sucker for Linus, he gives you his invitation. His pen is there on the desk, and you will need it for the football scene later.
If Charlie Brown asks you for a pen when you have already given it to him, you have some sort of major glitch, and may have to restart the island. Be sure that you have followed the correct sequence up to that point. (see related question)