How to get from Tokyo to Nikko and to Hakone?

I will arrive and depart from Tokyo for a 11 day trip in early November. I would like to travel to namely Nikko (1 or 2 days), Hakone (2 days), make day trips to Yokohama, Kamakura and Shibamata and spend the rest of the days exploring Tokyo. Do let me know if there are places along the way that I can fit in.

I am not sure how I should link these places and what passes to get as I am confused as Hakone and Nikko have their own passes too.

Based on the autumn leaves report, Nikko should come first before Hakone as I would like to view the autumn leaves at the waterfalls but how should I travel from Nikko to Hakone as the start and end point seems to point to Tokyo?

I am not sure how I should link these places and what passes to get as I am confused as Hakone and Nikko have their own passes too.

How to get to Hakone:
http://www.japan-guide.com/e/e5206.html

How to get to Nikko:
http://www.japan-guide.com/e/e3805.html

Travel between Hakone and Nikko leads via Tokyo.

You need to go through Tokyo to travel between Nikko and Hakone :)

As you seem to be planning to travel only in and around Tokyo (not leaving the Kanto region), you should not be getting any nationwide JR Pass or anything of the sort.

You can buy "NEX and Suica package" at Narita Airport if you want to - that gives you a good discount on Narita Express going into Tokyo and Suica prepaid card for local transport.
You can buy Hakone Free Pass by Odakyu Railway, and Tobu Railway's pass for Nikko.

Hi AK,

I will only be travelling within the Kanto region as I am travelling with my mum and with her pace, we will not be able to venture too far in 11 days.

Argh... it has been confirmed the only pass I can get for Nikko is the All Nikko Pass.

I will arrive in Narita Airport at 12 noon and I am thinking if we should travel to Nikko on this day. Can I ask if there is anything or anywhere to visit in Nikko in the evening since we should arrive in the late afternoon if we decide to travel there upon arrival in Tokyo?

Other options would be to spend the day exploring Asakusa and stay there for the night and travel to Nikko the next morning or travel to Yokohama by Nex and stay at Asakusa for the night and travel to Nikko the next morning. Which option should we take in order to maximise time?

There are multiple ways to get to Nikko and Hakone from Tokyo. So you need to specify where in Tokyo you start from and if you have a kind of JR Passes.

The JR and Tobu Nikko station area has nothing to do in the evening. You can find hotels, department stores, restaurants, etc. in Utsunomiya, the capital city of Tochigi prefecture, on the way from NRT to Nikko by JR.
http://www.jnto.go.jp/eng/location/regional/tochigi/utsunomiya_city.ht...

If you need to watch out that your mom doesn't get tired from a lot of traveling, following is my recommendation:

I will arrive in Narita Airport at 12 noon and I am thinking if we should travel to Nikko on this day. Can I ask if there is anything or anywhere to visit in Nikko in the evening since we should arrive in the late afternoon if we decide to travel there upon arrival in Tokyo?
Unless you (and she) plan to, and enjoy a stay at a hot spring ("onsen") inn, not really.

Other options would be to spend the day exploring Asakusa and stay there for the night and travel to Nikko the next morning or travel to Yokohama by Nex and stay at Asakusa for the night and travel to Nikko the next morning. Which option should we take in order to maximise time?

Again if you need to watch out for your mom's pace, cutting across from east (Narita) through Tokyo to west (Yokohama) with your luggage, and exploring there, then traveling across to the eastern part of Tokyo (Asakusa) sounds too rushy.
I would go straight to Asakusa, relax a bit, and then set off to Nikko the next day.

Hi CC,

Actually, I thought that we could travel from Tokyo to Nikko and from Nikko to Hakone but I realised it is not possible. We would have to return to Tokyo first before setting off for Hakone.

We will set off from Asakusa to Nikko and we do not have a JR pass.