Brutas has joined in the conspirators.

Brutus here is portrayed as something of a Judas figure. The sense of betrayal of friendship is overwhelming. "Casca is the first to stab Caesar. It is fitting that Brutus be the last. Caesar’s words to him—Et tu Brutè? (and thou, Brutus?)—indicate his disbelief that his friend could do such a thing." (http://www.enotes.com/julius-caesar/act-iii-scene-1-summary-analysis)

Caesar's last words have significance in a couple of different ways.

1.  Caesar is not surprised by Cassius's part in his assassination.  Cassius had sided with Caesar's enemy Pompey and held a grudge against Caesar when Caesar gained the ultimate victory over Pompey.  Caesar's line in Act 1 about Cassius having a "lean and hungry" look demonstrates his suspicion of the ringleader early on.  Some of the other conspirators such as Metellus Cimber dislike Caesar because of his treatment of their friends and family.  In contrast, Brutus was a respected Senator whose family had a long line of political involvement, and many historians believe that Caesar respected and appreciated Brutus.  He saw him as a friend, and Brutus's difficulty in deciding whether to join the conspiracy illustrates his overall positive feelings toward Caesar.  Thus, Caesar is surprised and devastated that someone such as Brutus has taken part in his downfall.

2.  Some historians recorded that Caesar had had a relationship with Brutus's mother.  Of course, that evokes many "yo mama" jokes, but undeniably, Caesar's alleged affair would have affected Brutus in ancient times just as it would affect a son today. No one wants to see his mother disparaged or the subject of gossip.  Some rumors even circulated that Brutus was Caesar's illegitimate son and that that is why Brutus stabs Caesar in the groin.  Of course, that is just speculation, but it makes for an interesting connection to Caesar's last words.

Since Marcus Junius Brutus was a teen, his uncle, Julius Caesar, had been carrying on an affair with his mother, Servilia. Added to this relationship, Caesar considered Brutus a beloved nephew. Further, while Shakespeare portrays Brutus as noble-minded, the historical records point to Brutus as more politico than appears in the play. For instance, Brutus sided with Pompey the Great against Caesar in the civil war in spite of the fact that Pompey had killed his father.  

So, when the shocked Caesar asks, "Et tu, Brute?" [Latin for "And you, Brutus?] he expresses surprise that his beloved nephew would stab him, knowing also that his mother loves Caesar. He should not, however, have been surprised at any lack of loyalty on the part of Brutus since he previously sided against him with Pompey. On the other hand, Shakespeare has been known to have changed historical fact in other history plays, so in this play Brutus's relationship with Pompey may not factor into the motive for killing Caesar.

In William Shakespeare’s play Julius Caesar, the character of Marcus Brutus is alone among those conspiring against the increasingly dictatorial Caesar in acting reluctantly and only because he believed the assassination was vital to the survival of the Roman republic.  While Cassius, Trebonius, Ligarius and the other members of the Senate involved in the conspiracy act  out of less altruistic motives, Brutus holds firmly to the belief that Caesar’s autocratic ambitions bode ill for the quasi-democratic nature of the existing political system.  In this, he is entirely sympathetic to the notion of eliminating his old friend and colleague.  During the conversation when Cassius is attempting to recruit him for the deed, Brutus concedes that public support for the demagogic leader is reaching alarming proportions:

“What means this shouting? I do fear, the people
Choose Caesar for their king.”

It is Brutus’ honor and general sense of loyalty – traits known by Caesar – that makes him an unlikely coconspirator.  It is in this context that, as the assassins close in for the kill, the mortally wounded Caesar, recognizing the participation in his assassination of one so honorable, utters the classic line, “Et tu, Brute! Then fall, Caesar.”  It is Brutus’ involvement in the scheme to murder him that leads the fallen, dying leader to lament the treachery while accepting its apparent inevitability.

The literal translation is: Even you, Brutus? Basically, it is the ultimate betrayal by one's closest friend. This scene, in which the conspirators in the Senate assassinate Caesar, comes after the audience has just witnessed the arrogance and hubris of Caesar, who compares himself to the gods. Brutus, a friend of Caesar who loves Rome more, has joined the conspirators in the assassination, a betrayal which is captured by the three words above.

Then Fall, Caesar means that he will fall both as a man and also as the ruler of Rome.

Marcus Brutus was a dear friend of Julius Caesar.  Even Brutus himself felt bad that he was involved in the plot to assassinate Caesar because he really had nothing personally against him.  In Act II, Scene i, of Julius Caesar by William Shakespeare, Brutus faces a conundrum in deciding what should be his steps for the good of Rome.

 After Cassius tries to enlist Brutus into the plot to assassinate Caesar, Brutus has to have time to think.  He loves Caesar as a friend, true Roman hero, and great general.  On the other hand, as a public servant, Brutus’s has as his first priority the good of the Roman Republic and the Roman citizens. 

In trying to make up his mind to become a part of the conspiracy, Brutus spent many sleepless nights trying to find logical reasons for joining the conspiracy. 

His final reasons involved these analogies:

1st

Think of Caesar as serpent seen in broad daylight.  The smart person would avoid it and keep from being stung.  If it is not avoided, then the serpent might bite the passerby and he would die from its venom.  This might be Caesar if given too much power.

2nd

Think of Caesar as though he is a serpent still in its egg in the nest.  As long as it remains in the egg, the serpent is harmless.  If it hatches, it will be dangerous.  So kill the snake while it is still in the egg.  The same is true of Caesar.  Kill him before he has so much power that he would be able to harm the Republic, the senators, and the people.

So, somewhat reluctantly, Brutus joins the conspiracy based on the possibility that Caesar might grow too powerful.

In Act II, Scene ii, the conspirators along with Antony show up to escort Caesar to the Capitol and later the senate.

Brutus is there as well.  Caesar seems somewhat honored that these men should come to accompany him calling them all friends.  He takes special note of Brutus and that he is honored that he has arisen so early to come with him.  Brutus also gives an aside in which he notes that Caesar may not want these so-called friends so close to him.

In Act III, Scene I, the conspirators have planned to present a case to Caesar and have him speak about it as they surround him and then stab him.  Brutus presents the case of Publius Cimber.

Brutus:

I kiss thy hand, but not in flattery, Caesar,

Desiring thee that Publius Cimber may

Have an immediate freedom of repeal.

 Then Cassius speaks up. All moving closer to Caesar ironically as he speaks that he is as great and constant as the Northern Star. Suddenly, Casca strikes the first blow; then all of the conspirators except for Brutus begin to stab Caesar.  He is stabbed at least 36 times.  Finally, Brutus walks toward Caesar with his dagger out.  Caesar in the final throes of death sees Brutus and in Latin states: “Et tu, Brute!”  And you, too Brutus.

Caesar felt that he could trust Brutus. Other than Antony, Brutus was probably he closest ally in the Roman government.  Hs inclusion into his death certainly would have surpised Caesar and greatly saddened as well.  Marc Antony says it well: This was the unkindest cut of all. 

According to Marc Antony who was not present, this burst Caesar’s heart and he fell ironically at the foot of Pompey, another great leader that Caesar had been responsible for killing. This ends the assassination.  The next move by the conspirators will be to wash their hands and dip their napkins in the blood of Caesar. 

The line "et tu Brute" is said by Julius Caesar himself. The rest of the line is "Then fall, Caesar." The line appears in Act III, scene i. After persuading Caesar to ignore the ominous dreams of his wife, Calphurnia, the conspirators accompany Caesar to the Capital. They use the pretense of a petition to draw close to Caesar without suspicion, asking Caesar to pardon Publius Cimber, the banished brother of conspirator Metellus Cimber. Kneeing, the members of the conspiracy beg Publius's pardon. Caesar's response is what they expect - Caesar, as constant as the sun cannot do as they request. From their kneeling positions, they each stab Caesar. Brutus's, who is a dear friend and confidante of Caesar, wound hurts Caesar the most, causing him to exclaim, "et tu, Brute," or "And you, Brutus?" Thus falls Caesar.