The MRTC subsequently received a build-lease-transfer agreement from the DOTC, which meant that the DOTC would acquire ownership of the system after the 25-year concession term. In the meantime, the DOTC would assume all administrative functions, such as regulating tariffs and operations, leaving the MRTC responsible for building and maintaining the system, as well as purchasing spare parts for trains. The MRTC will later transfer responsibility for system maintenance to the DOTC in November 2010. In return, the DOTC would pay the MRTC`s monthly fee for a number of years to reimburse the costs incurred.  The ban is in line with Circular No. 004 of the Office for Transportation Security`s Memorandum No. 004 of 2019 as well as the safety rules of the rail system. Due to the line`s high ridership, a proposal considered by DOTC and NEDA proposed to double current capacity by purchasing additional light rail vehicles for more than 520,000 passengers per day.  In February 2012, the line allowed folding bicycles to be transported on trains, provided the wheels did not exceed 20 inches (51 cm) in diameter.  However, problems arose in 2012 as maintenance resulted in train failures, lack of spare parts and neglect, and the system experienced numerous interruptions and accidents. This, in turn, has led to a decline in ridership, frequent unloading of passengers and inconvenience to passengers.
 The first train was scheduled to enter service by April 2016, but delays in its 5,000-kilometre (3,100-mile) trial delayed its deployment to scheduled service.   The trains were cancelled on the 7th. May 2016.  The line is owned by Metro Rail Transit Corporation (MRTC), a private company operated in partnership with the DOTr under a build-lease-transfer agreement. With nearly 550,000 passengers per day when MRTC`s maintenance service provider, Sumitomo Corporation of Japan, took over maintenance of the system, the line is the busiest of Metro Manila`s three rapid transit lines, built to critical standards such as accessibility and the use of contactless card tickets for easy passenger access. The total passenger volume far exceeds the maximum capacity of 350,000 passengers per day, with various solutions proposed or implemented in addition to the purchase of new vehicles to reduce chronic congestion. During construction, the CTMR oversaw the design, construction, equipment, testing and commissioning, while the DOTC oversaw the technical supervision of the project activities covered by the BLT contract between the DOTC and the MRTC. DOTC also sought the services of SYSTRA, a French consulting firm, in terms of technical expertise, experience and track record in construction and operation.  The project was revived in 1989 as a light rail project, originally known as the LRT-3 project. It was to be tendered as a build-operate-transfer project, with Hong Kong-based EDSA LRT Corporation winning the public tender for the construction of the line in 1991 under the administration of President Corazon Aquino.  However, construction could not begin because the project stalled as the Philippine government conducted several investigations into alleged irregularities in the project contract.
 In 1995, the Supreme Court upheld the legality of the project, paving the way for construction to begin under the administration of President Fidel V. Ramos.  A consortium of local companies, led by Fil-Estate Management, was later supported by Ayala Land and 5 others, who later formed the Metro Rail Transit Corporation (MRTC) in June 1995 and acquired EDSA LRT Corporation.  On July 12, 2021, the rail operator allowed passengers to bring pets with face masks on the line, but pets must be placed in a carrier bag before boarding a train, even as the Delta COVID-19 variant spreads throughout the country.  The use of face shields is no longer mandatory on public transit later in November 2021, unless an area is below the two highest levels of the alert level system.  Social distancing measures have also been taken.