Besides the crowded conditions, personalities came into conflict. Religious differences played a part in the tensions. The Whitmans were Presbyterians, while some of the newcomers were Congregationalists. One of the differences in doctrine involved the celebration of communion. The Whitmans felt that grape juice or even water served with the bread was appropriate, that these were symbolic of the blood of Christ. However, the Congregationalists preferred to use wine. Narcissa, who was pro-temperance, was very upset by the use of wine even within a sacramental context. She felt that all "spirits" were bad. Not only did the Whitmans frown on the use of wine, but one of these newcomers used tobacco!!! Elkanah Walker chewed and had the nerve to spit in the fireplace. This was in bad taste of course, partly just the idea, but also because the ashes from the fireplace were saved to make lye for soap making.

It proved to be a long, unhappy winter in cramped quarters. Fortunately with the arrival of spring, the new missionaries could continue their journey to their permanent mission stations.

In 1839 the first of the independent missionaries arrived. Two families, the Munger's and Griffin's were without support from any church or missionary group, planning to work alongside the missionaries already in the Oregon country. They were unsuccessful, as they had no financial support, and had to work in order to feed their families. Munger, a carpenter, was a big help to Whitman who was building the larger mission house, but all in all, it could be said that the independent missionaries were a failed venture.

The next year, six more independent missionaries arrived. This time, Narcissa was acquainted with one of the wives, although this did not lessen the problem of placing these workers in the missionary field of the Northwest. It was a foreshadowing of what was to come, the door of Old Oregon ever widening. On October 9, 1840 Narcissa wrote to her mother: "We are thronged with company now and have been for some time past and may be through the winter…As we are situated, our house is the missionaries' tavern, and we must accommodate more or less the whole time." Fortunately, by this time the new house was complete enough for these visitors to use, which helped relieve overcrowding and tensions.

In the fall of 1840 the first wagons made it over the Blue Mountains. They were reduced to the bare chassis but as Whitman said: "O you will never regret it. You have broken the ice, and when others see that wagons have passed, they too will pass, and in a few years the valley will be full of people."

In 1842, Elijah White was able to secure an appointment as a sub-agent of Indian Affairs for Oregon, and with a party of 19 wagons headed west to take up his duties. At Fort Hall the wagons were left and the party continued, all, including women and children, riding horseback. The Hudson's Bay Company saw White's arrival, along with his appointment as Indian Agent, as a very worrisome turn of events, and the London headquarters instructed Dr. McLoughlin not to recognize him or whatever authority he might try to exert. Once again, it was a glimpse of things to come.

The 1843 wagons rolled across this vast country to the cry of "Westward Ho!!!" and the term of "Oregon Fever" was popularized. Whitman took note of what was happening and was delighted.

Estimates of the numbers of the 1843 immigration vary. Whitman claimed it was 200 men. This first organized migration had the assistance of Whitman who was returning from his 1842 trip east. At that time, many assumed the trail ended at Fort Hall. When they arrived at Fort Hall, the immigrants discussed whether they should try to go all the way with wagons, or leave them. According to Perrin Whitman, Marcus's nephew who had accompanied him from New York, Whitman gathered the immigrants and told them that he would get them to the Columbia River if he lived; that they could stay with their wagons and follow him; he would get them through the Blue Mountains.

The winter of 1843 found the mission crowded with immigrants. Living in the mission house were:
The Littlejohn family with their new baby in the Whitman's bedroom.
The Whitmans and the two little girls who lived with them in the dining room.
Jesse Looney, his wife and 6 children and 1 single man in the Indian room.
The John East family with 4 children in the school room.
A French Canadian man in the Kitchen.
Perrin Whitman and David Malin (a foster child) in the attic.
Helen Marr Meek and Mary Ann Bridger were with the Littlejohns.

This brings the total population of the mission house to 24 family members plus one mountain man. The emigrant house housed 12 immigrants and two hired men. This brought the total population of pioneers living at Whitman's Mission to 41, 30 of whom were immigrants or mountain men.

The year 1843 set the example of what was to come. Each year the numbers varied, with 30 to 60 extra people swelling the population of the mission station. The immigrants needed food, but in 1843, this was sometimes in short supply. Narcissa describes the scanty fare in a letter dated January 31, 1844: "Potatoes, cornmeal, with a little milk occasionally, and cakes from the burnt wheat." Whitman had to ask for supplies from Henry Spalding, saying "Our living has to come from Mr. Spalding's. We live almost entirely without bread, having little flour and prospect of less until harvest. We have nearly consumed three of the largest & fattest oxen already which we got from Mr. Spalding & now have to look to the Indians for more."

Having learned the lesson well, the following year Whitman planted more potatoes, vegetables, and other crops. With the help of Mr. East, he re-built the grist mill with a new set of 40 inch stones. He expected to sell flour for $5.00 per 100 lb. if unbolted, or $6.00 if bolted. Unsifted meal would be priced at $4.00 per 100 pounds or $5.00 if sifted.

The 1844 travelers began to arrive Oct. 1 – 1500 in all, and later than usual due to a late spring. Many were sick or had new babies in their families. Narcissa complained to her parents: "I cannot write any more, I am so thronged and employed that I feel sometimes like being crazy, and my poor husband, if he had a hundred strings tied to him pulling in every direction could not be worse off."

The new arrivals included a blacksmith, a hatter, two Methodist ministers, a teacher, and the seven orphaned Sager children.

Whitman could not nor would not turn anyone away. Also the American Board of Commissioners for Foreign Missions expected the mission stations to be as self supporting as possible; the sale of supplies was an important source of income. Whitman gave credit or traded labor for supplies if necessary. Many people could not or would not pay for their supplies, leaving Whitman without compensation. After the trail moved farther south, many continued down the Umatilla, bypassing Waiilatpu. Some thought supplies would be available at The Dalles, often there were none there. In 1845, Whitman took a load of flour to the Umatilla River, asking $8.00 for unbolted, but was disappointed in the sales. He took in less than $150.00, $15.00 on trust, 3 cows and 2 steers in trade.

That winter there were fewer families wintering over. Three men, all "mechanics" -- one millwright, one chairmaker and wheelwright, and one blacksmith, were all useful to the mission station.

Josiah Osborn, the chairmaker, worked for supplies given at the rate of $1.50 per day. Given in produce was:
25 pounds of flour @ 5 cents per pound - $1.25
1 bushel of beets - 40 cents
1 bushel of potatoes - 40 cents
69 pounds beef - $3.79 ½
8 squashes - $1.00
20 pounds pork - $1.40
1 pound sugar - 20 cents
51 pounds meal - $2.04
6 feet tobacco - 60 cents

The Osborn family went on to the Willamette valley in 1846, but returned at Whitman's urging in 1847. They were to become well known as the family that hid under the schoolroom floor and escaped after the Indian attack on the Whitmans.

Fewer sales the next year, 1846, meant that the mission was not self supporting. Only six families wintered over, along with several single men. Whitman established three families and some of the men at the sawmill cutting rails. Narcissa wrote: "Set the table for more than twenty every day three times - and it is a pleasing sight." The winter of 1846-47 was very cold with deep snow that was hard on livestock. Many were lost, a hardship for both pioneer and Indian.

The immigration of 1847 was larger than the year before, but very unorganized. By August 23, more than 80 - 100 wagons had already passed. The Osborns returned, agreeing to work for an annual salary of $300.00. A measles epidemic broke out, and began to cause deaths among the Indians. By the end of the immigration season, the mission was very crowded, with 75 people, including 45 children living in the mission buildings. Fifty-two of these had crossed the mountains in 1847.

Two of the families in residence were employed, Mr. Saunders as a teacher and Mr. Young and his sons at the sawmill. The Smith family also went to the sawmill later.

The Oregon trail without a doubt had a great impact on Whitman's Mission, both pro and con. It provided a market for goods and services that Whitman needed so he could earn much needed income. He was sometimes accused of selling his goods at too high a price, but compared with other places he was either the same or cheaper. Some immigrants had the mistaken belief that they could get supplies cheaper at the Dalles, when in fact there were few if any available, and some suffered from this mistaken information. Whitman never turned away anyone for lack of ability to pay. His sense of Christian charity and duty would not allow him to deny help to anyone, and he often housed and fed those in need at his own expense.

Ultimately, it could be said that the Oregon Trail led to his death. The large number of people passing through, Whitman's involvement with them, and finally the measles epidemic all had direct connections with the trail. These events contributed to the attack on the mission station and the deaths of the Whitmans.