This is a good question, but the best answer is choice number two. Europeans were usually greeted with good will and curiosity by the indigenous people, but when the Europeans began to try to take control most cultures offered various degrees of resistance rather than submission.
In Africa this resistance took place in the form of guerilla and conventional warfare, depending on the political structure of the area in question. In sparsely populated places the people resorted to guerilla warfare since they didn't have the resources to match up with their invaders in conventional style battle. In areas with more advanced political structures direct military engagement was organized. The greatest example of this would be the success of Ethiopia in maintaining their independence. When faced with mounting pressure from the Italians they raised an army of 100,000 soldiers to keep their freedom.
The New Zealand Wars that took place in the middle of the 19th century saw the Maori's gain fame as fearsome warriors in the defense of their traditional lands versus the British.
Finally, history is full of examples of conflicts between European explorers and colonists as they tried to claim the lands in the Americas. The British, Dutch, and French all met heavy resistance in North America while the Spanish encountered the same problems throughout their Empire to the south.