make their final runs
オリンピックが開かれる前に交通網の利便性を高めるという内容です。
Tokyo transit system to be boosted before Olympics
Japan's land and transport ministry is planning to make improvements to Tokyo's transit systems connecting Haneda airport with the city center before the 2020 Olympic Games.
As a first step, the ministry will launch an experimental project for late-night airport bus services departing from Haneda airport after 1:00 AM. The project will start in October.
Currently, some international flights arrive at Haneda after midnight, but buses and trains already make their final runs before the late arrivals.
Ministry officials are exploring ways to accommodate additional international flights arriving at or departing from Haneda airport after midnight.
They consider it crucial to make improvements to transit systems connecting the airport to Tokyo's center.
http://www3.nhk.or.jp/nhkworld/english/news/20140106_04.html
記事の中に出てくる” make their final runs”は,「最終便」と訳せると思います。深夜まで羽田に到着する飛行機があったとしても,終電時刻やバスの最終運行時刻を過ぎているということです。
Run’sと複数形になっているため,「電車,バス,モノレール」などのあらゆる交通機関の運行が終わっているというニュアンスが読み取れます。(Ume)