The dark side was the belief that the white man had the right to destroy anything and anyone ( mostly Indians ) who got in the way.
Manifest Destiny expressed the philosophy that drove 19th century U.S. territorial expansion. It was an idea that God destined the U.S to spread out across the continent of North America because the U.S. had the best people, culture and religion.
The dark side of this legacy was the mass destruction of tribal organizations, confinement of Indians to reservations and killing of many innocent people. It contributed to the war with Mexico, where Mexico was defeated and much of its territory taken away. The killing was justified by the wrong belief that the territorial expansion was preordained by God as a way to spread American values and virtues across the country.