Morphy Defence in Ruy Lopez I don't get the point of Morphy's Defence in the Ruy Lopez opening:




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1. e4 e5 2. Nf3 Nc6 3. Bb5 a6



If White's purpose was to exchange Bishop for Knight and take the e5 pawn after it loses its defender (plus create some pawn weaknesses for Black), then the 3...a6 move comes too late to prevent it. Likewise I don't get White's retreat in all the variations that follow except for the exchange variation.
The basic idea of the opening was to snatch e5 pawn, but by playing Qd4 or Qg5 Black returns the pawn with good play. 

This forced White to seek other ways of reaching advantage, so he tried with Bxc6 counting on a won pawn endgame. However, things are not so easy since Black has ample of compensation in his bishop pair-remember that bishops are good in open positions-and doubled pawns control a lot of important squares. 

Since that try failed, White needed to try something else, and the only option left is bishop retreat. If they play Bc4 Black can transpose into Italian game with the extra temp since a6 has been played. Since a6 is an important move in those lines for Black, he would gain a small plus from the bishop retreat. That leaves Ba4. 

With this retreat White keeps pressure on e5 pawn and hopes to force Black into making some concession. Black will do his best to develop and defend without weakening himself but in the end he fails to do so. He must play b5 at some point to release the pressure from the White light-squared bishop. After b5 Black will have  compromised pawn structure on the queen side ( backward c pawn and exposed b5 pawn ) and that is the concession White hoped for. 

It isn't much-Black is still OK-but it will guarantee White a long initiative-which is better overall result than what other lines offer. 

The reason for this being Black's c-pawn is blocked by a knight so he can't participate in the battle for the center. This enables White to seize initiative in the center by forming d4+e4 pawn center supported with the c3 pawn. Black will lose time to reorganize his queen side in order to counterstrike which gives White time to meet comfortably Black's plan. This usually involves Nbd2-Nf1-Ne3/Ng3 maneuver, preparing king side attack, but can be a4 thrust, or simply a favorable change of the pawn center's type-he can block the position with d5 or open it with an exchange like dxe5 or dxc5. 

The last option is the most dangerous for Black so he needs to play very passively for a while before he counter-strikes.

In this Wikipedia link you can see the list of variations. Notice that in the main line there is one thing in common for all the Black's responses-they regroup their queen side to meet White's initiative.

To conclude:

By retreating the bishop to a4 White gains small concession from Black in view of compromised pawn structure which results in White's better control of the center, which results in small but lasting initiative.

Hopefully this answer sheds some light for you.

If you have further questions leave a comment.

Best regards.