The Atlantic Terminal, known as Flatbush Avenue through 2009 is the Brooklyn Terminus of the LIRR and its Atlantic Branch. After major renovations that began in 2002 along with the renovations to the subway station and the building of the new Atlantic Terminal shopping complex construction was finally finished in January 2010 as a plaque in the waiting room says, dedicating the terminal to 'Brooklyn: The Long Island Rail Road's Birthplace in 1836' with the opening of the new grand glass entry pavilion and atrium that overlooks the Southwest corner of the odd five-way intersection between Flatbush Avenue, 4 Avenue, Hanson Place and Ashland Place in the middle of downtown Brooklyn. The Atlantic Yards, a 12 track LIRR train yard that were until the mid-2000s exposed to the surface is now covered by the Barclays Center, the new home of the New Jersey Nets basketball team. Building a stadium at that site is a long time in the making, over fifty year ago the Brooklyn Dodgers wanted to build a domed baseball stadium at the same location. The arena is diagonally across from the LIRR station and there are signs directing attendees of the safest walking route to cross the busy streets to reach it. There are entrances from street level to the LIRR station at each side of the main atrium (from Hanson Place and Flatbush Avenue) as well as another along the Flatbush Avenue storefronts of the Atlantic Center Shopping Mall. This entrance is complete with an LIRR Blue awning like it is a store. There is also a direct entrance into the first floor of the mall, and from 2 Hanson Place
Two main staircases in the atrium and an elevator (that is one of two ADA elevators into the Subway station in addition to a street elevator at Pacific Street) lead down to the underground (but lit by light from modern atrium) concourse where there is a direct entrance to the subway and the Manhattan-bound (2,3) IRT Local platform (use for other subway lines) and a passageway up a few steps to an entrance to the Brighton BMT (B,Q) platform. There is also a small waiting room with modern benches, restrooms, and 4 ticket windows (3 were open when I visited in October 2012 during the PM rush hour).
The waiting room leads out to the end beyond the bumper blocks of three LIRR island platforms that serve for the six tracks. These were recently renovated with lighted signs that say Atlantic Terminal along both platforms. Track 6 is far shorter than the rest of the tracks because that platform ends early to allow space for the direct IRT Manhattan-bound 2,3 subway entrance. There are also little glass opaque cubes from the subway station to the LIRR platforms. Each platform has an additional staircase down to it from the street level floor of the entrance pavillion, near the Atlantic Center end. All three platforms also have staircases up from the subway passageway that connects the BMT Brighton Line B,Q platform to the IRT Brooklyn 2,3,4,5 platforms. These staircases each end in a bank of subway turnstiles directly on the LIRR platform for tracks 3,4,5, and 6. The staircase for tracks 1 and 2 leads down to two high entrance turnstiles next to an MVM. There are even LIRR track information signs along this connecting passageway within the subway station, so transferring passengers can leave the subway system at the right staircase to catch their trains.