After his commanding officer orders the massacre of innocent Indian Brave women and children, Nathan Algren (Tom Cruise) shuns the army and hits the road ... and the bottle. Offered an easy training job far away in Japan, he accepts the position but things aren't quite what they seem.
  Leading raw recruits into battle, Cruise stands his ground courageously and is soon face-to-face with the feared Samurai warriors and their strong warrior code.

So just who is the last samurai?

After Tom gains the friendship of the Samurai people, he goes with them to the capital and is offered his old job again.  But he's too outspoken against the regime and is soon in danger from watcful assassin-henchmen.
  Meanwhile the Samurai clan leader Katsumoto talks with the Emperor about his ideas, but is turned down and put into the local jail.  Cruise knows he will take his own life, so convinces his friend to escape instead through a message delivered by his little reporter pal (Timothy Spall).
  Tom has some intuitive-flashback style fight with 4 or 5 assassins and, using his new found sword skills, cuts them all to pieces.  He escapes to meet with the Samurai boys and plan the last big fight.

He walks out wearing the red armor of the fella he killed earlier, and the angry guy slaps him on the back, so everything is alright.  Suddenly he's promoted to second-in-command it seems too.
  For the big fight, both sides line up - most of the army from the first battle (without poor Billy) on one side, with a few more cannons and machine guns.
  The Samurai have a Plan A - luring half the enemy into a fake retreat 'oldest trick in the book' trap.  To finish off the rest they race their horses towards the big guns --- but the enemy commander orders the men to take them out, and none of them make it past the wall of bullets.
  Katsumoto is injured badly, and Tom helps him to end his life 'honourably'.  Tom was just shot in the leg, unlike everyone else.
  The Japanese army respect the courage of the Samurai and salute them.

So, it seems Tom Cruise was the Last Samurai.  Rather than moan about it or join an exclusive club with Chingachgook, he meets with the Emporer just before he is to sign the important contract and tells him how Japan should honor the Samurai, and gives the Emporer the sword that belonged to Katsumoto.

The fat little enemy commander complains, but the Emperor eventually pipes up and tells him that all his land will be given away - and if he wants to talk back he can end his own life in an honourable way.

The movies tells us they don't know what happened to the American in history - but in the movie we see him go back to the village to get busy with the wife of the poor guy he murdered a while back.