Usual plan to go to Fuji involve staying at the base/at the logde in the mountain. Depends on what your goal is, watch sunrise, sunset or just want to climb. 

The usual and most common plan for first time climber, if you want to see the sunrise: 

1. Get a ticket by bus (highway express) from Shinjuku station, 

2. from Tokyo go at around 3pm, it will take around 2 hours to go to Fuji 5th station(base for you to climb), 

3. Climb through Yoshida trail (yello trail), that is the easiest trail and it has a lot of lounge, huts to rest and toilets, 

4. The standard time to reach the summit is around 6 hours. The trail consist of sands, rocks and uneven surface. If you clinb at night, be sure to bring headlamp with you since you will need your hand to crawl the rocky trail. (Seriously, I feel like Frodo Baggins who tries to climb Mount Doom).

5. Bring winter clothes if you climb at night, even when you are climbing at daylight, you could never tell the weather. Bring light jacket, wind stopper, rain coat with you. The top of Fuji-san could be very cold, when I was there in July, I saw snow on the top of the mountain. 

6. The descend route is faster, it requires around 3 hours to descend. Its mostly consisted of sand, and just be careful on your way down. If you descend at night, you may require more time since you will be exhausted. 

7. You could take 9am or 10 an or 11 am or 3 pm or whatever time convenient for you by bus to go back to Shinjuku. 

Shinjyuku, 

7/27/2015

resources:
http://www.garyjwolff.com/climbing-mt-fuji.html