Due to budget, time, and other setbacks, the line underwent several modifications. For instance, Sur 69 and Vía Láctea stations were not built due to neighborhood opposition. Ganaderos station was rejected by the
National Institute of Anthropology and History because its construction would have affected a nearby archaeological site. Francisco del Paso station was canceled because its construction would have caused a six-month partial closure of
Line 8; instead Atlalilco station was chosen as the interchange station and as a consequence it has the longest passenger transfer tunnel in the system. These issues caused the route to be changed. Instead of running along Arneses Avenue (
Eje 3 Oriente) and later along Canal Nacional Avenue, the route was moved instead to run along Tláhuac Avenue (Ejes 9 and 10 Sur). ESIME Culhuacán and La Vírgen stations were relocated and became
San Andrés Tomatlán and
Lomas Estrella stations, respectively. Between Atlalilco and San Andrés Tomatlán,
Culhuacán station was added to the route. Construction of the first leg of the line,
Tláhuac–
Atlalilco, started on 23 September 2008. The section was replanned as an
at-grade route to be later modified to a combined at-grade and
elevated section. The second stretch of the line, which runs underground from Atlalilco to
Mixcoac, was finished in April 2012. The line was built by a consortium comprised by ICA Group, Carso and Alstom. The project suffered multiple construction delays, and its $1.3 billion cost was a 50% overrun.
Inauguration Starting on 16 June 2012, the STC allowed riders to have access on Sundays to test the service and to familiarize them with the stations and route. The line began daily service on Monday 24 September 2012, and it was officially inaugurated on 30 October 2012 by
Marcelo Ebrard,
Head of Government of the Federal District from 2006 to 2012 and
Felipe Calderón,
President of Mexico from 2006 to 2012.
Temporary partial closure In an unprecedented event in the history of
Mexico City Metro, Line 12 had to be shut down temporarily in the stretch
Tláhuac–
Atlalilco due to severe faults in its infrastructure. This section is the one that corresponds to the elevated stretch of the line. The technical and structural faults of the elevated stretch caused the trains to run on the verge of derailment, due to wear on the rails that provoked slopes and damage to the tires of the trains, putting six out of the 30 trains out of service. Previously, on October 27, 2015, the stretch
Periférico Oriente–
Culhuacán, resumed the service, but all trains stopped at Periférico Oriente station till the service on the whole line was reestablished.
2017 earthquake On 19 September 2017, a 7.1 magnitude earthquake hit
Mexico City and other zones of Central Mexico, affecting Line 12 with electrical power shortages and the derailing of a train between the
Nopalera and
Zapotitlán stations. Due to this, and potential damages to the line's infrastructure, service in the
Tláhuac–
Culhuacán section of the line was suspended. After evaluations, it was determined that the line had visible damages in the tracks and structural faults. Therefore, the stretch from Olivos to Tláhuac was closed for repairs. Service in all the closed stations was resumed on 30 October 2017.
Expansion In 2017, an expansion for Line 12 was announced. Construction started on 29 November 2017. The extension was expected to be completed by 2020, but works were delayed, thus, being projected to open by 2021. This project will extend the line from
Mixcoac to
Observatorio, where it will connect with
Line 1 and it will have three new stations and a length of . The two new stations are Valentín Campa and Álvaro Obregón, both situated in the
Álvaro Obregón borough. The totality of the extension is being constructed underground and is expected to open in December 2023. The original 1985 and 1996 plans for Line 12 considered the line going westward from Mixcoac with two new stations, as in the undergoing expansion. Nevertheless, the connection with Line 1 at Observatorio was not planned in the projects.
2023 partial reopening of elevated section On 15 July 2023, the stretch between Periférico Oriente and Culhuacán reopened. ==Route==