A young orphaned undercover detective on suspension learns from an FBI agent that his biological father's is their current target.

How is his suspension causally germane to his being assigned to the new case? And if he's assigned because he knows the suspect, what happened to the discovery that it's his father?

And if he's on suspension

He's not sidelined. The story begins with him being approached by the agent while on suspension. He's not with the FBI initially but is pulled in because of his relationship with their target.

I agree. Bring the detective in on the action. If he's your "hero", why have him sidelined?

Correction: When an FBI agent discovers...

When an FBI discovers that his suspect under surveillance is his long lost biological father, he must decide whether to betray his father or betray his oath.

The father is a criminal worthy of prosecution. The son after informed of the news must decide if he wants to help take his own father down or after getting to know him (under cover) tip him off and possibly suffer some consequences. Morale dilemma indeed.

Why is the FBI hunting down his father? Is the father an innocent victim of a witch hunt or a perp who deserves to be brought to justice?

Why does the son turn on the FBI to protect his father? Is there a moral dilemma in the story? Should there be one?

I appreciate your feedback and will consider it.

I like this idea something about the primal urge to protect ones own blood works very well in it.

But with economy in mind I would say lean up the protagonist description; ditch 'young' and 'undercover'. Also you didn't direct the the main action very well. I think in the logline the exact mechanism by which he comes to be motivated is secondary to the action he will take. Also the action as well as its descriptions seam a bit bland lacking potential for major action, stakes and dilemmas.

just a punt at it:

When an agent learns he must protect his father from his boss, he wages a one man war against the FBI in an attempt to stop the nation wide man hunt.