Visit the ornate UNESCO-listed Toshogu Shrine and nearby Rinno-ji; many shrine areas open ~8:00–17:00 — arrive early to avoid crowds and enjoy autumn foliage.
Take a bus to scenic Lake Chuzenji and the Kegon Falls observation platform — buses run regularly and the falls viewing elevator is typically open ~8:30–17:00.
Return toward the station area to visit the Nikko Tamozawa Imperial Villa (if open) or pick up local crafts and yuba products in shops near the station.
Take a short train/bus to Arakurayama Sengen Park for the iconic Chureito Pagoda view of Mt. Fuji — best early for clear air and fewer people (park open 24/7).
Visit the Itchiku Kubota Museum (beautiful kimono textiles and gardens, typically open ~9:30–17:00) or stroll the lakeshore for photos, cafés and boat rentals.
Board an afternoon/evening bus back to Shinjuku (journey ~2 hours). Book seats in advance for peak season and check sunset times for last-minute photo stops.
Take a sightseeing pirate-ship cruise on Lake Ashi and ride the ropeway for views of Owakudani and (when clear) Mt. Fuji; ropeway and cruise hours normally ~9:00–17:00 but Owakudani can close for volcanic activity — check status.
Visit volcanic valley viewpoints and try the famous black eggs if Owakudani is open (it closes sometimes for emissions), or relax in a public onsen / hot spring facility like Yunessun (check opening hours).
See the iconic Kamakura Great Buddha statue and visit Hasedera temple with its gardens and views; most temples open ~8:00–17:00 (seasonal hours possible).
Short ride to Yokohama to visit Minato Mirai, the CupNoodles Museum (hands-on exhibits) and the waterfront — CupNoodles Museum usually open ~10:00–18:00 (last entry earlier).
Early visit to Tsukiji Outer Market for fresh sushi, grilled seafood and market atmosphere; many stalls open early and close by early afternoon (check shop hours).
Stroll Ginza for upscale shopping and cafes, or walk around the Imperial Palace East Gardens (generally 9:00–16:30; closed certain weekdays — verify before going).
Experience the famous Shibuya crossing and head to a Shinjuku viewpoint (e.g., Tokyo Metropolitan Building observation deck open ~9:30–23:00) for city skyline shots.
Depart for the airport allowing ample time for check-in and security; Narita Express ~1h from Tokyo Station (JPY3,190), Haneda by monorail/limousine bus ~30–60 minutes (costs vary).
Board your flight home. If your flight is later, you can squeeze a short visit to Odaiba or teamLab (confirm opening times — teamLab often 10:00–19:00).