Silph Co.

The Silph Co. is located in the middle of Saffron City.  You can’t gain access to this building until you save Mr. Silph from Team Rocket inside the Pokemon Tower in Lavendar Town.
 
 There are a lot of teleporters in this building and I advise going through all the floors to defeat all the enemies and to pick up all the items.  Here’s a quick guide and some pictures to get to the end.
  1. Hop in the elevator and head to the 5F.  The Card Key will be in the bottom hallway or in the room in the southwest corner.
  2. Once you have the Card Key, hop back on the elevator and head to the 3rd floor.  Open the door on the left side of the hall way and enter the first teleporter.
  3. Now that you’re on the 7th floor, defeat Gary and go into the next teleporter.
  4. Now you’re on the 11th floor.  Defeat Team Rocket, talk to Mr. Silph, and be rewarded the Masterball and you’re all done.