Deceit is a major theme in this story, and it comes across in different ways. First there is the deceit of Lola and Paul Marshall. Although it is not totally explored, Lola must have known the identity of her assailant. Paul had attacked her in the children's room in the Tallis family manor before dinner. Later, he rapes her (or that is what Lola claims). But Paul keeps silent while Robbie is taken to prison. Later Lola and Paul are married, and they never confess their lie.
Briony too is deceitful. One could argue that she is shaken by what she witnessed and could not distinguish the difference between truth and what she imagines. But there are too many circumstances that go against this theory. For one, Briony suffers from guilt. She would not feel guilty if she had not consciously lied.
There is another type of deceit at the end of the novel, when the author twists the story around and insinuates that the so-called true story that he was presenting was actually created by one of his characters, Briony. When Briony tells the readers that this is her novel, she argues that it is her fictionalized creation and she can create any kind of ending that she wants. She can have Cecilia and Robbie die in the war or she can have them live happily ever after. It is the prerogative of the author to decide what is true, in the sense of the story, and what is not. This is the deceit of the fiction writer.
War is another theme. There is the war of nations and the subsequent author's statement of how despicable and wasteful a war can be. There is also the war within the Tallis family. Cecilia refuses to have anything to do with her family because they did not trust Robbie. In some ways, there is also the war inside of Briony's head. She knows she has done something terribly wrong, but she is not strong enough to face the consequences of her confession until it is all but too late. She wants to perceive herself as a good person, so she becomes a nurse for the wounded soldiers. She tries to atone for her transgression, but this does not give her the peace that she truly desires.
There is also an overtone of class issues. The Tallis family is well off, and although they appear to be tolerant of people around them, there is a definite attitude of their being better than most, in particular the Turner family, Grace and Robbie. Mr. Tallis has supported Robbie's education but this an act of charity for someone who is of a lower class. Meanwhile, Mrs. Tallis looks upon Robbie suspiciously, as if he were crazed, whereas she sees no such telltale signs in Paul Marshall (the man who rapes Lola), because he is rich.