Mr Stephenson said he discovered that in 2002, New Zealand Special Air Services (SAS) troops were involved in passing prisoners to local authorities. The prisoners were beaten "so badly one became crippled", Stephenson said.
In April 2010, Mr Stephenson visited an Afghan Crisis Response Unit (CRU) to speak with an Afghan Colonel about the New Zealand SAS troops.
After that meeting, he wrote the articles, which raised questions about what the New Zealand troops were doing in the war zone, he said.
Stephenson told the court he arrived at the base with his driver and interpreter.
He said his driver had an unobstructed view from the car to the base entrance, where he could see Mr Stephenson and his interpreter had gone into the facility.
While he walked through the base, Stephenson saw a New Zealand flag flying and a wooden building with a Maori carving over the entrance, which indicated to him New Zealand troops were based there.
Mr Stephenson gave the court a detailed description of the base and of the people he spoke with.
The Colonel, referred as Colonel B to protect his identity, "was a rather short gentleman ... and he was dressed in a dark green uniform with black flecks or stripes".
In notes he made during his interview, Colonel B was complimentary about the SAS members and spoke of missions SAS troops had been on, including one where the troops had detained five people during an alleged attempted suicide mission, Mr Stephenson said.
"He showed me mugshots of five detainees, which had their fingerprints on them.
"He told me information about the operation, which I reported in the article.
"Before then I had no knowledge of that."
Mr Salmon told the jury the Defence Force didn't like the articles Stephenson had written about the SAS soldiers.
After the Metro article ran in April 2011, NZDF produced a statement and released it to media organisations which "attacked the man" and said he invented his trip to the CRU base, Mr Salmon said.
The NZDF said they had evidence he was turned away from the base and Mr Stephenson had not produced any evidence he had been there, the court was told.
Technically, Stephenson was turned away from the base, but that was the previous day to his successful trip, Mr Salmon said.
Mr Salmon said the Defence Force now admits Stephenson might have gone to the base for the interview, but they have never taken down the statement from their website because technically it was correct.
The ordinary New Zealander looking at that statement would not be able to connect the time Mr Stephenson was turned away with the following day when he was allowed into the base, he said.
Stephenson said the statement attacked his credibility as a reporter.
He told the court he offered the Defence Force evidence of his trip to the CRU base, including note paper that would have had Colonel B's fingerprints on it.
"They have not taken me up on that offer, nor have they taken me up on the offer to supply intricate details that would show I had been to the base."