I'm walking around the Marunochi area for Run with the Wind (Kaze ga Tsuyoku Fureiteiru). These scenes where during their participation on Hakone Ekiden, a university relay marathon that usually held during the first week of January.
If you have no idea about Hakone Ekiden, it is a long distance running relay from Tokyo to Hakone, and vice versa. So each of the team where placed on different sections in between those places. The route of the marathon almost goes along the Tokaido Line so our characters might rode this line going Tokyo Station.
From the final episode scenes, the other members met each other at the Marunochi North Exit at Tokyo Station.
The starting and finishing line of Hakone Ekiden is located at the south side of Yomiuri Shimbun Building. I visited this place on May so trees around the area has already grown leaves (will revisit this during winter)
*pilgrimage made last May 18, 2019