Just reward for foolishness
This is the story of two people whose romantic relationship falls apart because they got involved with each other for all the wrong reasons.
When Jenna D'Sora wonders aloud why she doesn't fall for someone like Data and then kisses him, the emotionless android ponders, on this minimal encouragement, whether to pursue a relationship with her. After asking advice of all and sundry, he does. And then both he and Jenna discover that Data's unique nature does not make romance an easy prospect.

"In Theory" tackled the subject of Data and romance very well, I thought. It's a sad tale, as we see Jenna's growing disillusionment with Data, and her painful realisation that she did not know him, or herself for that matter, as well as she thought she did. The lack of impact the whole business has on Data is a pointed lesson in itself.
In the other story thread, the Enterprise finds itself in difficulties on account of the mysterious "dark matter" surrounding it. It's a competent plot, but nothing special. And why does Picard always insist on doing the flying himself? Where are all the young hot-shot pilots with superior skills to those of their ageing captain?
It's nice to see that Data has friends and interests beyond the command crew, and you really do feel for him and Jenna as what seems to have been a very comfortable friendship is destroyed. But they are both very silly people. Jenna seems to have been convinced that Data had hidden depths to be discovered, and is quite definitely on the rebound. And Data's motivations seem all selfish; he seems to have no better reason to romance Jenna than "because I can". Perhaps that was another lesson about the character - thoughtlessness and an abysmal lack of understanding can still be possible for Data after so long amongst Humans.
I do find "In Theory" a difficult episode to watch. Data's behaviour makes me cringe, it is so awful. But it is a good episode; thoughtful, well-written, and moving.

In Theory Data's emotions aren't real
"In Theory" emotionally unavailable men aren't good at relationships

Take a guy like Data and the poor Ensign Jenna Anaya. She has a thing for men who are emotionally unavailable. I have to say why did you think Data could provide any real emotion? Before his emotion chip was available this romance was doomed from the start.

The Dark Matter part of the story is much better. While Data is attempting to get in touch with his feelings; parts of the ship start vanishing. There is a good part in this one where Picard has to travel through the nebula to stop the Dark Matter.

The Best stories are those about people's personal lives
Data has always been my favorite character of any star trek series. I've always liked those episodes that delt more with the personal lives of the crew rather than some planetary problem. Here, There are moments that are both interesting and histarical! For instance, people who know the Data character know that he never yells for no reason, but when he is told that all couples fight, he starts a fight with his girlfriend for no reason just because he thinks he is susposed to. It doesn't get much more funny than that.

P.S. MR. BERNADO! I am interested to know that name of that novel where Wesley finds out about Datas' program. If you could tell me I would happy. Thank you.=)