HIMYM AU: Barney finds out that Robin works for S.H.I.E.L.D as Agent Hill (Part 2)
What Barney didn’t know is that Robin begged Coulson’s team to inject the GH-325 drug into his system to prevent him from dying years ago. She promised to look after him for the rest of his life and look out for possible negative side effects of the drug, without Barney ever finding out about any of it since it’s a classified, SHIELD-member-only information. Scared that one information may lead him to another, and scared of where he may end up in, Robin did what she thinks is best when she found out he knew about her identity as Agent Maria Hill: She distanced herself away from him so he could go on with his life as she look after him and keep him safe from afar.
…. I might accept this as an explanation for their breakup.
"The only hope you have is to accept the fact that you’re already dead. The sooner you accept that, the sooner you’ll be able to function as a soldier is supposed to function: without mercy, without compassion, without remorse. All war depends upon it."