They passed through several small Mexican towns before arriving in Albuquerque on October 5. In most places the Mexicans were not welcoming, but the Indian populations were eager for trade. They explored the immediate vicinity around Albuquerque. Lieutenant Ives was supposed to meet them there with supplies, but he arrived one day after their arrival. This, plus the fact the soldiers were busy battling Indians, delayed the expedition four weeks. He used the time to catch up on his notetaking and test some new instruments brought by Ives.
They left once the military was free to supply them with new animals and give directions. Whipple sent Sherburne and others south to explore the Rio Grande, while Whipple headed directly west. The two groups met on November 14 and followed the San Jose River and crossed the Sierra Madre Mountains. On November 20, they reached a Zuni village that had been nearly wiped out by smallpox. Whipple met with town officials and collected Zuni vocabulary words. He also made numerous notes on Zuni customs and culture.
The group reached the border of modern-day Arizona on November 29 and six days later reached the Little Colorado River. Some troops from a nearby fort joined them there. Some of this terrain was very rough with volcanic soils and peaks. The temperature was now below freezing at night and one time it was only reached 9°F.
