The allegations seemed simple: One of the Army’s most promising officers covered up a corruption probe to curry favor with the White House. But internal correspondence between two of the leading U.S. generals in Afghanistan paints a more complicated picture. The officer in question may have invited the probe he’s accused of blocking.

Lt. Gen. William Caldwell, who until recently supervised the training of Afghan soldiers and police, is accused of obstructing an inquiry into widespread corruption within the Afghan military’s medical staff. Caldwell allegedly scolded his staff for inviting the Pentagon inspector general to join a probe that would occur at a politically sensitive moment — the eve of U.S. congressional elections. President Obama himself “calls me Bill,” Caldwell is alleged to have boasted.

But in correspondence with Afghanistan war commander David Petraeus, provided exclusively by Danger Room by a source sympathetic to Caldwell’s case, the general appears to propose bringing the Pentagon investigator in. And during a House Armed Services subcommittee on Tuesday, the Pentagon inspector general’s office backed Caldwell up.

A comprehensive inquiry into Afghan National Army medical corruption was “beyond the expertise and capability” of Caldwell’s command, Caldwell emailed Gen. Petraeus on October 29, 2010. “Therefore, would like to make a recommendation that we look to some other entity, perhaps an independent entity such as the DoDIG SPO [Department of Defense Inspector General Office of Special Plans & Operations] to conduct this inspection.”

“We have a good working relationship with the DODIG from past inspections,” Caldwell continued, “and believe that they would give us a thorough and helpful look vice a witch hunt that other oversight agencies may execute in these circumstances.” Petraeus replied, “Good idea, Bill.”

Petraeus added that he wanted to see one of the most troubling Afghan military officials, command surgeon general Col. Zia Yaftali “prosecuted and not just promoted upstairs.” Caldwell replied, “we did initiate that action, along with several other steps, several weeks ago.”

In a December 2011 memo that Caldwell’s former subordinate, Air Force Col. Schuyler Geller, provided to a congressional oversight panel, Geller accused Caldwell and his top aides of yelling at Geller and colleagues for informing the inspector general of a pattern of misconduct exhibited by Afghan army’s medical staff. “You should have known better!” Caldwell allegedly shouted at Geller during a tense meeting in late October 2010. With an election coming up, such an inquiry could damage the White House, Caldwell supposedly told his subordinates.

But a source sympathetic to Caldwell’s situation denies that the general sought to protect Obama. Caldwell had minimal contact with the White House during his two years in Afghanistan. “In order to damage a relationship” with the president, the source says, “you have to have a relationship.”

The source adds that Caldwell was indeed “very upset” with Geller — but not for the reasons Geller believed. Caldwell thought that immediately involving the Defense Department inspector general in a probe of the Afghan military would undercut and embarrass the Afghan minister of defense, Abdul Rahim Wardak, a key U.S. ally.

“Have you informed the [Afghan] Ministry of Defense? Have you informed Gen. Petraeus?” Caldwell supposedly asked Geller, according to this source. “This is an embarrassment to the Afghans — can you imagine the embarrassment to Minister Wardak? You know how Afghan culture is — it’s all about saving face.”

This source acknowledges that Caldwell may have discussed the U.S. election cycle, as Geller alleges. “If he said something like that, it was to ask us if we had thought through the 2nd and 3rd order effects,” the source says. Caldwell is “savvy enough to know that a DOD IG investigation isn’t going to change the [congressional] election.”

In the e-mails obtained by Danger Room, Caldwell indeed does not propose going to the inspector general as rapidly as Geller’s memo argued was warranted. But he proposed doing so after sending a top deputy, Maj. Gen. Gary Patton, to “meet with Minister Wardak on Tuesday and again address this issue, and I will meet with him on Wednesday to reinforce,” according to a follow-up email Caldwell sent Petraeus on October 30.

“After the engagement with Minister Wardak I do want to formally request the DoD-IG/SPO Medical Team to conduct an Assistance Visit to examine the systems that we have for U.S. purchase, Afghan distribution, storage, and accountability of pharmaceuticals for the ANSF [Afghan National Security Forces],” Caldwell continued. “Additionally, will ask DoD-IG/SPO to assess the personnel resources, financial, and contractor oversight of NTM-A/CSTC-A [the NATO command for training Afghans] Medical Training Advisory Group (MTAG) and supporting systems.”

Geller favored an even broader investigation than that, however. According to Geller’s December 2011 memo, the Afghan military medical corps received their assignments due to political and family patronage, not merit. Geller’s memo suggested that such hiring practices led to corrupt Afghan doctors diverting pharmaceuticals to the black market.

It’s possible that Caldwell sent the e-mails to Petraeus as a maneuver to save himself embarrassment — or even reprisal. Geller had already alerted the Pentagon inspector general to the problems within the Afghan military medical corps, which he alleged put Caldwell in the awkward position of having to rescind a request for outside assistance. All that occurred before Caldwell’s e-mails to Petraeus, which are dated Oct. 29 and 30, 2010. So perhaps this is an elaborate CYA maneuver. Caldwell has yet to speak publicly about the episode.

But if that’s the case, the Pentagon inspector general’s office doesn’t have a problem with Caldwell.

During a House Armed Services subcommittee hearing on Tuesday afternoon, Amb. Kenneth Moorefield, the Pentagon’s deputy Pentagon inspector general for special plans and operations — the official Caldwell recommended to Petraeus ought to assist in an inquiry into Afghan military medical corruption — testified that Caldwell had requested Pentagon help two weeks after the episode Geller described. On Nov. 10, 2010, Moorefield told the congressional panel, Caldwell asked his office for aid in a “countrywide review of the entire logistical system” for Afghan army pharmaceuticals. Rather than feeling stymied by Caldwell, Moorefield testified that his team’s arrival in Afghanistan, around Thanksgiving 2010, set “probably some sort of record for a response to any request we’ve ever received.” A follow-up investigation occurred in February 2011.

Not everyone on the panel was satisfied by Moorefield’s testimony. Rep. Mike Coffman (R-Colorado) said he considered it “stunning” that Caldwell is “still serving today in the U.S. Army after all that’s occurred here.”

The Pentagon’s top Afghanistan policy official, David Sedney, defended Caldwell to the subcommittee, saying the general’s leadership helped begin to “turn around what had been a broken system.” Moorehead added that the beleaguered Afghan military’s medical system would continue to face “ever-present” challenges. But the hearing didn’t include testimony from the two officers who can resolve the issue: Air Force Col. Schuyler Geller and Army Lt. Gen. William Caldwell.