The SRTS project provided for seven "links", i.e. interchange stations where commuters would be able to seamlessly transfer from one line to the other. When the program was initiated four links were in use. The Santa Mesa and Recto Link were added in April 2004, when the already under construction Purple Line became fully operational. The Northrail project has been cancelled in September 2012, as a result the Caloocan Link is missing and the common station project has been cancelled in January 2013, as a result the North Avenue Link is dropped. The closing of the loop has almost been completed by extending the Yellow line with five new stations, unlike originally outlined by the plan. The Yellow would require one more station make a connection via the so-called North Avenue Link to North Avenue MRT Station. In order of operation the following links have been realized:
The project aimed to unify fare systems on the lines through the use of contactless smart cards, similar to the Octopus card in Hong Kong and the EZ-Link card in Singapore. The integrated system has not been implemented, as the project was dropped. A weekly ticket which is valid on LRT-1, MRT-2 and MRT-3 lines has been introduced in 2004 though. For ₱ 250 one can make an unlimited number of rides per day on LRT-1, MRT-2, and MRT-3 lines during one calendar week with the so-called Flash Pass Card.