When upgrading your ship, you should bring the needed variety of Upgrade Modules to Penguin Pete at the Outpost's Shipyard. When the player has enough Upgrade Modules in their stock, the (?) pursuit marker will show over Penguin Pete's head. Tossing the Upgrade Modules out of the player's stock will not get rid of the (?) mission marker. Merely drop the Upgrade Modules from your stock at a safe range, and after that talk with Penguin Pete to upgrade your ship. You can then gather your dropped Upgrade Modules and repeat the procedure for all subsequent ship upgrades. (version 1.0.5)