After you recon the instructions should say to put any cards for any city not on the grid in the reserve. The reserve is for items not currently in play. Once you connect a city to the grid then the city card goes in the player discard pile and the infection card goes into the game end area.
And you may want to edit the title so it doesn't spoil the fact that cities will be unconnected when you discover them.
And you may want to edit the title so it doesn't spoil the fact that cities will be unconnected when you discover them.