WASHINGTON — Since his early days in office, Patrick Shanahan has butted heads with secretary of the Air Force Heather Wilson over the Pentagon’s future space architecture.

But a new inspector general investigation into the acting secretary of defense — released Thursday, and clearing him of any wrongdoing in regards to pushing products from his previous employer, Boeing — shows the tensions existed at a different level than previously reported.

Of the 33 witnesses interviewed by the IG’s office, including former Secretary of Defense Jim Mattis, the joint chiefs, and other top Pentagon officials, Wilson was the only one to raise red flags about Shanahan’s behavior.

“None of the other witnesses told us that they had any concerns regarding his adherence to his ethical obligations. Many reported that Mr. Shanahan was attentive to his ethical obligations,” the IG wrote.

While Wilson raised concerns about Shanahan’s actions, others in the Pentagon interviewed by the IG noted that the former executive was preemptive in avoiding what may be conflicts of interest.

Air Force Chief of Staff Gen. David Goldfein, for instance, said there were two cases when the KC-46 tanker started to stray into a conversation, and that Shanahan “actually interjected and said, ‘We have to stop the conversation.’ And one of those times he actually got up and said, ‘Hey, I do understand you need to talk about this, so I’m going to depart.’”

But Wilson, who has announced her intention to leave the Pentagon next month and return to academia, has repeatedly butted heads with Shanahan over space issues, in particular over the formation of the Space Force and the Space Development Agency over the last eight months.

Sources familiar with the relationship describe it as tense, between two people who seem to have personal distaste for one other.

Wilson’s concerns came from three areas. The first, Shanahan’s potential role in a decision to accept the KC-46 tanker despite ongoing issues from manufacturer Boeing; second, a December meeting between Shanahan and Elon Musk, the CEO of SpaceX; and third, whether the former executive shared classified information from Boeing programs improperly.

“I felt in a difficult ethical position myself in that case,” Wilson said, via the IG, of the meeting between Shanahan and Musk. "That one directly involved [Mr. Shanahan]. The other [KC-46 and classified matter] may be just sloppy staff work, but I think at least on one occasion, I felt uncomfortable.”

Despite these three concern areas, Wilson did tell the IG she felt Shanahan mostly acted properly when talking about his past with Boeing.

“It’s not as though he touts Boeing as a company … I don’t recall him saying something specific about Boeing,” Wilson is quoted as telling the IG. “In almost every meeting there were references to the Dreamliner. And I never really took those issues as being any kind of an ethical problem.”

Wilson also stated that Shanahan may have said, “’We would never have done it this way. Or we wouldn’t do it this way,’” adding: “It was more comparing his experience and criticizing a contractor that he felt wasn’t getting the supply chain right.”

She later told the IG that she never had a discussion with Shanahan about buying the F-15X, a Boeing-made jet.

The concerns

The first concern raised by Wilson came at the end of 2018, when the Air Force was debating whether to accept the first KC-46A tanker from Boeing, despite ongoing issues with the plane. Wilson indicated there was pressure from Shanahan or his office to just accept the plane.

Wilson “expressed concern to [the IG] that Mr. Shanahan or his staff may have created the appearance of favoritism” for Boeing by asking Ellen Lord, the undersecretary of defense for acquisition and sustainment, to chair a meeting about the tanker, as well as the fact Shanahan’s office had received a copy of a memo meant for Mattis. She also raised concerns after Shanahan’s staff asked her to coordinate with Mike Griffin, the Pentagon’s research and engineering head, on the tanker issue – despite the KC-46 not directly being in his portfolio.

On Dec. 28, Wilson “noted to her staff Mr. Shanahan’s recusal and expressed her concern that Mr. Shanahan’s office had received a copy of her memorandum. Ms. Wilson also told her staff that she would decide on the next steps herself, and directed Air Force personnel not to participate in an OSD meeting that Mr. Shanahan’s chief of staff suggested Ms. Lord should convene.

Eventually, a decision was made by Will Roper, the Air Force’s acquisition head, to accept the planes; Roper told the IG that “the allegation that Mr. Shanahan pressured the Air Force to accept the KC-46 was ‘absolutely untrue.’”

Per the IG, “None of the documents we reviewed indicated that Mr. Shanahan received Ms. Wilson’s information memorandum, asked questions of any involved parties, expressed an opinion, issued guidance, made a recommendation, or otherwise participated in the matter of the Air Force acceptance of the KC-46.”

The Musk complaint dates to a Dec. 6, 2018 meeting between Shanahan and Musk. At the time, Musk’s SpaceX was in competition with Boeing over a launch contract. Per the IG, Wilson told Shanahan she did not think he should meet with Musk, and when the meeting went ahead, she shared her concerns about the meeting with Thomas Ayres, the Air Force general counsel.

Ayres, in turn, reached out to the Standards of Conduct Office (SOCO) to inquire whether they saw an issue with the meeting. However, Shanahan’s team had already reached out to SOCO weeks ahead of the meeting and received clearance as long as acquisition issues were not directly discussed.

That information “allayed” Ayre’s concerns and “he later told this to Ms. Wilson,” the IG report reads. The IG found nothing foul occurred in the meeting.

The details on the classified matter are, unsurprisingly, thin. But it appears Wilson raised concerns about Shanahan’s comments regarding a Boeing program that is related, in some way, to the classified issue being discussed. However, after talking with three other witnesses, the IG found no issue with Shanahan’s comments.

“In this case, Mr. Shanahan’s comments were about general DoD capabilities and did not constitute a recommendation or decision about a particular matter involving Boeing,” the IG concluded. “Secretary Mattis made a decision about the particular matter separately and without Mr. Shanahan’s input. Mr. Shanahan’s comments did not violate his ethical obligations.”