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So I was medically discharged from the ITC Para back in 2014 for a Grade 2 stress fracture, I was told then in my med board that I WAS able to rejoin in 1 years time. So I waited a year and began the rejoin process but my parents didnt want me to rejoin the army and pushed me into applying for the navy, I had to do a 3 month diary for them and get a letter off my GP then went for a medical, It was about this time that I decided to sack my parents and the navy off and apply for the army (paras again) but about 3 weeks after my medical I got a letter from the navy medical officer saying that I am permanently unfit join. So my question is will this affect my army application? All I had was a ONE grade 2 stress fracture in my right leg and I have had no further problems since then.

Firstly if you want paras, go paras. Nothing against the navy, but you need to do what you want!
Don't let anyone stop you.

I've had stress fractures in three of the four lower leg bones and it's never been a problem.
When stress fractures heal properly the area is usually stronger anyway.

As far as I'm aware the navy application process won't affect your army application. Just start fresh with the army.