The Phillies’ Noah Song will begin a rehab stint in the minors. And then what? That’s complicated.

CHICAGO — Noah Song is scheduled to appear in his first game this season Thursday on an injury rehab assignment for low-A Clearwater.

And if he was any other minor league pitcher, it would be a footnote.

But the Phillies picked Song in December from the Red Sox in the Rule 5 draft, which means the 26-year-old right-hander must be added to the active roster once he’s ready to pitch after straining his lower back in spring training. And he must stay there for at least 90 consecutive days or else be exposed to waivers and then offered back to Boston for $50,000, half the cost of selecting him in the first place.

It’s a complicated arrangement. But Song’s situation features another wrinkle: He hasn’t pitched competitively — or almost at all, really — since 2019 due to military responsibilities to the U.S. Naval Academy.

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The pertinent questions now: How will Song pitch after all that downtime? And what happens when his assignment is over after the maximum 30-day term?

“It’ll be interesting to see where he ends up,” Phillies manager Rob Thomson said Tuesday before the opener of a three-game series against the Cubs amid questionable air quality in Chicago due to the Canadian wildfires. “No doubt.”

If not for the Rule 5 restrictions, the Phillies could simply reinstate Song to the 40-man roster (he isn’t counting against it now because he’s on the 60-day injured list), call him up, and option him to a minor-league team, as they did recently with first baseman Darick Hall.

But Song must go directly to the active major league roster to be retained in the organization.

If the Phillies weren’t a playoff contender, it would be easier to carry a pitcher who hasn’t played above A-ball. It’s much more challenging for the defending National League champs, a win-now team with a nearly $250 million payroll.

So, Song will ramp up in the minors as a reliever, Thomson said. Never mind that all seven of Song’s professional appearances in the Red Sox’s system came as a starter. Or that he hasn’t pitched out of the bullpen since 2016, his freshman year at Navy. A relief role requires less building of arm strength. It also figures to enable Song to focus on his fastball and slider, while shelving his less-developed curveball and changeup.

“He’ll go two [innings], maybe two-plus at some point,” Thomson said. “He’ll have the back-to-back [games] eventually. We’ll treat him just like a regular reliever.”

There’s almost no precedent for what Song is attempting to do. Song has cited Mitch Harris, a right-handed reliever who got drafted by the Cardinals in 2008 and reached the majors in 2015 after a five-year commitment to the Navy.

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The Phillies acquired Song without knowing when — or even if — he would get clearance from the Navy to pitch. He wasn’t granted a waiver in 2020, and for 2½ years in flight school, he threw only infrequently and off flat ground, his baseball future dimming as the time passed.

But in late February, as Song prepared for a deployment to Japan, the Navy transferred his service to the reserves. He reported to spring training, began throwing, and got shut down with what the Phillies characterized as back tightness. He has been rehabbing in Florida ever since.

Thomson cited reports from the Phillies’ staff in Clearwater that indicated Song’s velocity has risen since he returned from the injury and certainly since he arrived in camp. In allowing two runs in 17 innings for a 1.06 ERA at single-A Lowell in 2019, Song topped out at 99 mph.

“It’s not to where it was, but it’s gone up and it’s gotten better,” Thomson said of the zip on Song’s heater. “There’s more crispness to his stuff as time has gone on.”

At present, Dylan Covey is the last pitcher on the Phillies’ roster. He made only seven appearances through 26 days since joining the team as a waiver claim from the Dodgers and lacks a defined role on the staff. But he’s 31 and has major league experience, so when necessary, the Phillies brought him into the fifth inning of a tie game (June 12 in Arizona) and the ninth inning with a two-run deficit (Saturday against the Mets.)

Would they trust Song in those spots? Could they? They have reliever depth stashed in triple A, with Connor Brogdon and Andrew Bellatti. What if they’re able to add even another reliever before the Aug. 1 trade deadline?

It all figures to come to a head by the end of next month. Unless Song gets injured again during the rehab assignment, a predicament that would stop the 30-day clock and rewind it to the beginning, the Phillies will have to make a decision on him by July 29.

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By then, there will be less than 90 days left in the season. But according to a league source, the Phillies would be allowed to retain Song as long as they kept him on the roster for the duration of the season and however many days spill over into next year to reach the 90-day mark.

Maybe Song’s performance will dictate what they do. Maybe they’ll just have to take a leap of faith.

Either way, it will be fascinating to watch.