The ruined store is a destroyed building in west Freeside that houses a soup kitchen run by NCR. It is located near Cerulean Robotics.
The only entrance is locked and requires a key to open. During the G.I. Blues quest there will be 2 NCR troopers standing outside the entrance. In order to enter the building to talk to Elizabeth Kieran you must pass a Speech check of 60 (or 30) from one of the troopers, you can pickpocket a key to the store, or you can obtain the password from the Missionary after answering his three questions to convince him you are an New California Republic (NCR) citizen. Inside you will find Squatters receiving free food and drinks from Kieran.
Finding the store is not easy if you rely on the Pip-Boy. Approaching it from town guided by just the compass markers will make it look like you are there already. To get there from the Silver Rush: looking out from the Silver Rush doors, face north, cross the street and enter the small destroyed building in which Bill Ronte is or had been sitting. Take the door located on the ground floor. On the other side, head North, and then turn left under the motorway bridge pillars. As you reach the burnt out car (next to the train tracks), turn left and follow the road heading South West, parallel to more motorway bridge pillars. The building is on the left hand side.
If you're having trouble, follow the train tracks towards the building with the barred up blue doors. The NCR building is opposite the South Eastern corner of this building, over that bit of rubble.