noun
Counter for two long, thin objects such as bottles, pens, trees, or legs. The reading にほん follows the standard counter 本 (ほん) with rendaku.
冷蔵庫にビールが二本ある。
There are two bottles of beer in the fridge.
この道には桜の木が二本植えてある。
Two cherry trees are planted along this street.
Means 'one (long cylindrical thing)'. 二本 is the specific counter for two such objects.
Means 'three (long cylindrical things)'. Note the reading change: 二本 is にほん, while 三本 is さんぼん.
Compound of 二 (に, 'two') and the counter 本 (ほん, used for long cylindrical objects). The reading にほん is regular, with 本 keeping its base reading ほん.