As the American armies advanced, more battles were fought, more thousands died on both sides, more thousands were wounded, more thousands sick with diseases. At one battle north of Chihuahua, three hundred Mexicans were killed and five hundred wounded, according to the American accounts, with few Anglo-American casualties: "The surgeons are now busily engaged in administering relief to the wounded Mexicans, and it is a sight to see the pile of legs and arms that have been amputated."

An artillery captain named John Vinton, writing to his mother, told of sailing to Vera Cruz:

The weather is delightful, our troops in good health and spirits, and all tidings look auspicious of success. I am only afraid the Mexicans will not meet us amp; give us battle, — for, to gain everything without controversy after our large amp; expensive preparations… would give us officers no chance for exploits and honors.

Vinton died during the siege of Vera Cruz. The U.S. bombardment of the city became an indiscriminate killing of civilians. One of the navy's shells hit the post office; others burst all over the city. A Mexican observer wrote:

The surgical hospital, which was situated in the Convent of Santo Domingo, suffered from the fire, and several of the inmates were killed by fragments of bombs bursting at that point. While an operation was being performed on a wounded man, the explosion of a shell extinguished the lights, and when other illumination was brought, the patient was found torn in pieces, and many others dead and wounded.

In two days, 1,300 shells were fired into the city, until it surrendered. A reporter for the New Orleans Delta wrote: "The Mexicans variously estimate their loss at from 500 to 1000 killed and wounded, but all agree that the loss among the soldiery is comparatively small and the destruction among the women and children is very great."

Colonel Hitchcock, coming into the city, wrote: "I shall never forget the horrible fire of our mortars… going with dreadful certainty and bursting with sepulchral tones often in the centre of private dwellings- it was awful. I shudder to think of it." Still, Hitchcock, the dutiful soldier, wrote for General Scott "a sort of address to the Mexican people" which was then printed in English and Spanish by the tens of thousands saying "… we have not a particle of ill-will towards you-we treat you with all civility-we are not in fact your enemies; we do not plunder your people or insult your women or your religion… we are here for no earthly purpose except the hope of obtaining a peace."

That was Hitchcock the soldier. Then we have Weems the historian:

Hitchcock, the old anti-war philosopher, thus seemed to fit Henry David Thoreau's description of "small movable forts and magazines, at the service of some unscrupulous man in power", it should be remembered that Hitchcock was first of all a soldier-and a good one, as conceded even by the superiors he had antagonized.

It was a war of the American elite against the Mexican elite, each side exhorting, using, killing its own population as well as the other. The Mexican commander Santa Anna had crushed rebellion after rebellion, his troops also raping and plundering after victory. When Colonel Hitchcock and General Winfield Scott moved into Santa Anna's estate, they found its walls full of ornate paintings. But half his army was dead or wounded.

General Winfield Scott moved toward the last battle-for Mexico City — with ten thousand soldiers. They were not anxious for battle. Three days' march from Mexico City, at Jalapa, seven of his eleven regiments evaporated, their enlistment times up. Justin Smith writes:

It would have been quite agreeable to linger at Jalapa… but the soldiers had learned what campaigning really meant. They had been allowed to go unpaid and unprovided for. They had met with hardships and privations not counted upon at the time of enlistment. Disease, battle, death, fearful toil and frightful marches had been found realities… In spite of their strong desire to see the Halls of the Montezumas, out of about 3700 men only enough to make one company would reengage, and special inducements, offered by the General, to remain as teamsters proved wholly ineffective.

On the outskirts of Mexico City, at Churubusco, Mexican and American armies clashed for three hours. As Weems describes it:

Those fields around Churubusco were now covered with thousands of human casualties and with mangled bodies of horses and mules that blocked roads and filled ditches. Four thousand Mexicans lay dead or wounded; three thousand others had been captured (including sixty-nine U.S. Army deserters, who required the protection of Scott's officers to escape execution at the hands of their former comrades)… The Americans lost nearly one thousand men killed, wounded, or missing.

As often in war, battles were fought without point. After one such engagement near Mexico City, with terrible casualties, a marine lieutenant blamed General Scott: "He had originated it in error and caused it to be fought, with inadequate forces, for an object that had no existence."

In the final battle for Mexico City, Anglo-American troops took the height of Chapultepec and entered the city of 200,000 people, General Santa Anna having moved northward. This was September 1847. A Mexican merchant wrote to a friend about the bombardment of the city: "In some cases whole blocks were destroyed and a great number of men, women and children killed and wounded."

General Santa Anna fled to Huamantla, where another battle was fought, and he had to flee again. An infantry lieutenant wrote to his parents what happened after an officer named Walker was killed in battle:

General Lane… told us to "avenge the death of the gallant Walker, to… take all we could lay hands on". And well and fearfully was his mandate obeyed. Grog shops were broken open first, and then, maddened with liquor, every species of outrage was committed. Old women and girls were stripped of their clothing-and many suffered still greater outrages. Men were shot by dozens… their property, churches, stores and dwelling houses ransacked.… Dead horses and men lay about pretty thick, while drunken soldiers, yelling and screeching, were breaking open houses or chasing some poor Mexicans who had abandoned their houses and fled for life. Such a scene I never hope to see again. It gave me a lamentable view of human nature,… and made me for the first time ashamed of my country.

The editors of Chronicles of the Gringos sum up the attitude of the American soldiers to the war:

Although they had volunteered to go to war, and by far the greater number of them honored their commitments by creditably sustaining hardship and battle, and behaved as well as soldiers in a hostile country are apt to behave, they did not like the army, they did not like war, and generally speaking, they did not like Mexico or the Mexicans. This was the majority: disliking the job, resenting the discipline and caste system of the army, and wanting to get out and go home.

One Pennsylvania volunteer, stationed at Matamoros late in the war, wrote:

We are under very strict discipline here. Some of our officers are very good men but the balance of them are very tyrannical and brutal toward the men… tonight on drill an officer laid a soldier's skull open with his sword… But the time may come and that soon when officers and men will stand on equal footing… A soldier's life is very disgusting.

On the night of August 15, 1847, volunteer regiments from Virginia, Mississippi, and North Carolina rebelled in northern Mexico against Colonel Robert Treat Paine. Paine killed a mutineer, but two of his lieutenants refused to help him quell the mutiny. The rebels were ultimately exonerated in an attempt to keep the peace.

Desertion grew. In March 1847 the army reported over a thousand deserters. The total number of deserters during the war was 9,207: 5,331 regulars, 3,876 volunteers. Those who did not desert became harder and harder to manage. General Gushing referred to sixty-five such men in the 1st Regiment of the Massachusetts Infantry as "incorrigibly mutinous and insubordinate."