For four innings Sunday afternoon, everything went according to the Pirates’ plan. Kevin Newman homered off Jon Lester to give them a lead in the first. Steven Brault worked three perfect innings. Chad Kuhl pitched a perfect fourth.

But the Bucs’ bats were quiet the rest of the way, and their second foray into extra innings went no better than the first. In four extra innings with the automatic runner starting on second base, they have scored zero runs. The Cubs were happy to capitalize on their mistakes as they handed the Pirates a 2-1 loss in 11 innings at Wrigley Field.

“It’s tough. With all the injuries that we had this series, it’s especially tough. But we’re right there,” catcher Jacob Stallings said. “It’s all you can ask for at the end of the game, to be right there and have a chance to win. We’re just not pulling ‘em out.”

• Box score

When manager Derek Shelton sat down for his postgame press conference, he quickly praised the work of his bullpen, looked into the laptop in front of him and deadpanned, “Probably nothing else to ask me about, right?”

Here are a few of the key decisions Shelton and the Pirates made as they lost their fourth straight game and their seventh in nine this season.

1. Taking out Brault
In Stallings’ view, Brault looked as good as ever as he struck out four while breezing through three innings on 35 pitches. Then, as part of Pittsburgh’s piggyback plan, Brault didn’t return for the fourth.

That Brault came out of the game was no surprise. The Pirates are slowly increasing his workload, and he has not pitched more than two innings since an intrasquad game last month. Pittsburgh is also trying to be cautious with every pitcher after a shortened ramp-up to the season.

Brault said the outing was “a display of what I can be there consistently going forward” and took no issue with his early exit.

“I understand Shelty’s trying to keep me healthy, trying to build me up. I’m totally down [with it],” Brault said. “I want to be a starter. I know he knows that. I feel like I'd rather be safe and make sure I don't aggravate anything.”

That’s especially true for someone like Brault, who was diagnosed in March with a strained left shoulder then eased back into action while baseball was shut down. They’ve seen pitchers throughout baseball go down early in the season due to injuries, including four of their own: Kyle Crick, Clay Holmes, Michael Feliz and Mitch Keller.

So while observers surely shouted that the Pirates should’ve let Brault keep pitching, the Pirates asked: Would it really have been worth risking his health for one more inning?

“The fact that he had only thrown two innings the last time because of the rain delay, no way were we going to extend it,” Shelton said. “The other thing is, when you tell the second guy [Kuhl] who has been trained as a starter that he’s going to get the fourth inning, he’s already started his ramp-up work and we don’t want anything to come in there.”

2. Calling on Kuhl
After an encouraging season debut last Monday, Kuhl pitched a clean fourth inning Sunday as the tandem starter behind Brault.

Then Kuhl, who repeatedly checked his pitching hand during his outing, gave up a run in the fifth on back-to-back doubles by Willson Contreras and Kyle Schwarber. Two batters later, Kuhl walked off the mound with director of sports medicine Todd Tomczyk due to an abrasion to the cuticle of his right index finger. Shelton and Stallings both said Kuhl’s fingernail issue came up during his outing, so there was nothing they could have done to prevent what happened.

“I had not heard that it was bothering him before,” Stallings said. “Stood with him during [batting practice] in the outfield yesterday for 45 minutes. He didn’t say anything.”

It hardly mattered, anyway, because Geoff Hartlieb, Dovydas Neverauskas, Nik Turley and Richard Rodríguez delivered one of the bullpen’s best performances of the season.

3. Pulling back Burdi in the ninth
The Pirates initially brought in Nick Burdi with the game tied in the bottom of the ninth. But then came a one-hour, four-minute rain delay. When play resumed, left-hander Sam Howard took the mound instead of Burdi. According to Shelton, the delay exempted Burdi from the three-batter-minimum rule.

It turned out to not be a significant issue, as Howard struck out three over two scoreless innings, and Shelton’s explanation fell in line with his previous handling of Burdi and other pitchers.

“We’re talking about a guy who’s coming off thoracic outlet [syndrome surgery] and Tommy John,” Shelton said. “He’s trending in the right direction and health is something that’s extremely important. So there’s no way we’re going to risk sitting for 40 minutes then throwing him back out there and having some risk of injury. It’s not worth it.”

4. Sending Stallings in the 10th
The 10th inning started with Stallings on second base as the automatic runner and Josh Bell slicing a pinch-hit single into left field. Third-base coach Joey Cora waved around Stallings, and the slow-footed catcher collided with Contreras in front of the plate for the first out.

With backup catcher John Ryan Murphy still available, why not pinch-run Gregory Polanco for Stallings? Shelton said Polanco was available, but the wet field and hour-long delay combined with Polanco’s injury history didn’t make for ideal circumstances to use him.

So then, why send Stallings home? If he had been held at third, the Pirates would have had runners on the corners with nobody out and the top of the order coming to the plate.

“I think we give more credit to Schwarber. He made a hell of a throw,” Shelton said. “I think Joey does a hell of a job over there. He’s aggressive. He’s consistent. I think he’s one of the better third-base coaches in baseball, so no problem with that send.”

Bell moved to second on Schwarber’s throw, but he was stranded there after Adam Frazier lined out and Newman hit a comebacker to reliever Ryan Tepera.

5. Running in the 11th
The Pirates began the 11th with Newman on second, José Osuna up and Colin Moran on deck. Osuna immediately hit a grounder to shortstop Javier Báez. With Newman running on contact, the easy play was in front of Báez, who threw the ball to David Bote to record the first out of the inning at third base.

“I think we have to be a little more aware of where Báez is on that play right there and also knowing how well Javy moves and how well he throws,” Shelton said. “We just have to be more aware in that situation.”

With one out and a slower runner on first, Moran lined out to center. Jarrod Dyson grounded out to second to end the inning.

6. Managing the bottom of the 11th
The Pirates sent right-hander Cody Ponce to the mound in the 11th inning to make his Major League debut in highly unusual circumstances. Anthony Rizzo led off with a flyout to right fielder Cole Tucker, allowing the automatic runner Bote to take third base. The Pirates could have intentionally walked Báez, potentially setting up an inning-ending double play, but decided against it.

Báez promptly ended the game with a walk-off single to center.

“We did talk through it. Then you’re getting to Contreras, and you’re also talking about a kid’s Major League debut,” Shelton said. “The last thing I wanted to do was put more traffic on the bases for him and put pressure on him for him to execute pitches.”