The lack of a railroad bridge over the Missouri River, made it difficult for the Union Pacific to comply with a provision of The Pacific Railroad Act of 1862. That act, signed by President Abraham Lincoln, specified the building of the railroad westward from Council Bluffs, Iowa; but that city was located on the east bank of the river, and no bridge existed to allow tracks to cross that wide body of water. Omaha, Nebraska, on the west bank of the river, became the actual starting point for the Union Pacific Railroad.
Council Bluffs had been chosen by Lincoln, partly on the advice of General Grenville Dodge in 1859. The grand plan was for feeder railroads to converge on Council Bluffs where their passengers, mail, and cargo would be transferred to the Union Pacific. In fact, the first feeder railroad from the east to reach Council Bluffs did not occur until January 1867. The lack of rail connectivity with the industrial centers in the east during the early construction years forced the Union Pacific to rely on riverboats to transport the bulk of their rails and rolling stock from the manufacturers to Omaha.
If you have read the sample chapters on this website for Eagle Talons, you know that Will Braddock, our protagonist, crossed the Missouri on the ferry when he arrived in Omaha in search of General Dodge in early 1867.