Can Brock Purdy And Kyle Shanahan Solve The 49ers’ Mike Macdonald Problem?

For the 49ers, Sunday’s game in Seattle is as big a Week 5 game as it can get. First place in the NFC West is on the line, and if the Niners can win it, they’ll have a multi-game lead in the division with tie-breaking wins over both the Rams and Seahawks. That’s a nice little cushion in the league’s most competitive divisional race.

San Francisco-Seattle games are always bitter, but the 49ers carry an extra layer of resentment into this tilt after how last season ended, with the Seahawks defense stuffing their offense in a locker twice in three weeks, including a 41-6 beatdown in the NFC Divisional Round.

It probably means a little more for 49ers coach Kyle Shanahan and quarterback Brock Purdy, who have spent the last few years tearing through defenses but always seem to struggle against Seahawks coach Mike MacDonald.

In their first matchup, when MacDonald was calling plays for Baltimore’s defense, Purdy threw four interceptions in a 33-19 loss on Christmas night that ended his MVP campaign back in 2023. Shanahan and Purdy got some revenge against MacDonald in their first inter-division matchup, a 36-24 win for the 49ers in 2024, but the Niners haven’t scored more than 17 points in any of the four games since. Three of those were losses, and San Francisco hasn’t scored a touchdown in either of the last two.

Macdonald has been Shanahan and Purdy’s boogeyman over the past few years. With him coaching a division rival, they can’t escape him. 

For the 49ers to take control of the NFC West (and the conference at large), for Shanahan to prove he’s still the league's best offensive mind, and for Purdy to firmly entrench himself in this year’s MVP race, they’ll have to get past Macdonald first.

So … can they do it?

Before we can even attempt to answer that, let’s look at why Macdonald’s defense has been an unsolvable riddle for Shanahan and Purdy. For a theory, let’s go straight to one of the primary sources:

"[It’s] how sound they are, yet [they’re] still aggressive," Shanahan said this week. "When they’re aggressive, they’re rarely irresponsible. It’s tough to get big plays on them. I think they’ve been no. 1 in the league two years in a row in that, whether it’s run or pass game."

Shanahan is correct. No defense has been better at limiting explosive plays over the last two seasons. And how they do it makes playing against the Seahawks defense such a miserable experience.

"They play out of a two-shell defense more than anyone in the league," Shanahan said. "Even when you get past the front seven, it’s tough to get past those safeties. Those safeties back up everybody for big plays – yet they’re still very aggressive, so it doesn’t feel like you can dink and dunk them the whole game."

Macdonald has built his defense in a way that allows it to enjoy all of the benefits of a bend-but-don’t-break approach without one key difference: this defense doesn’t provide its opponents any room to breathe.

The Seahawks’ zone-match coverage provides the best of both worlds. The sturdy two-high zone shell prevents throws over the top, but the "match" element lets defenders stick tight to routes. Even for a trained eye, it can be difficult to tell whether Seattle is in man or zone coverage. On any given pass snap, it looks like they’re playing both.

Seattle’s defensive approach is particularly effective for taking away the middle of the field and up the seams. That’s where the linebackers and safeties sit, looking to pick up receivers entering their assigned zones. Windows close rather quickly against Seattle.

One key to San Francisco’s consistent offensive success is Shanahan’s ability to pry open those windows with his play designs. Purdy’s been an awesome fit in the scheme because he’s willing and able to make those throws, which can be difficult for quarterbacks who lack top-end arm talent. Purdy may not have the 100 mph fastball, but he throws with anticipation – which buys him a few fractions of a second – and he can feather passes over defenders.

Shanahan makes good use of Purdy’s talents by calling a lot of high-low concepts over the middle. He’ll have a receiver run a short route about 5 yards deep, with another receiver running a deeper route that breaks or bends behind it 10 to 15 yards downfield.

Shanahan is a master at spamming the same concepts over and over, but from different formations and personnel groupings to keep defenses off his scent. Against the 30 other teams, Purdy can pepper that area all game. Since the start of the 2025 season, about a quarter of his attempts have targeted the small area between the numbers from five to 20 yards down the field. Here’s his passing map with that area of the field highlighted.

In the three games he’s played against Seattle, only about 12% of his attempts have targeted that same area.

And the difference in production is staggering. Per Pro Football Focus, Purdy’s averaging 5.8 yards per attempt and -0.88 expected points added per play against Seattle. He’s averaging 9.7 yards per attempt and 0.45 EPA per play. Even when those throws have been available, the Seahawks have rendered them ineffective.

In the three games against Seattle last season, Purdy averaged 5.8 yards per attempt on plays where he remained "in structure." That’s nearly 3 yards lower than his average against every other opponent. With the structure of Shanahan’s offense failing him – and his team down on the scoreboard – Purdy went into scramble mode, which … didn’t work very well either. The 49ers aren’t a team built for a heavy dropback passing game. They can do it when necessary, but it’s not their offensive aim, and Seattle makes it hard to play that kind of game.

San Francisco didn’t score a touchdown over their final 120 minutes against the Macdonald’s defense last season, so Shanahan and Purdy will want to avoid falling into that trap once again. But the first game offers a viable path to success for the offense. 

The Niners won that game, and while they put only 17 on the board, the offense moved the ball. They punted only twice, but Purdy threw two passes (trying to force it over the middle), and Jake Moody missed two field goals (one was blocked). 

Despite the interceptions, Purdy finished with an 85.5 QBR. That was the third-highest mark of his season and his second-best performance against a Macdonald defense.

Shanahan’s running game wasn’t overly efficient, but it wasn’t entirely useless. The 49ers didn’t have to abandon the run at any point – the running backs logged 31 carries – allowing the offense to stay on script. San Francisco’s shotgun usage is a good health indicator for the offense. 

When San Francisco is using shotgun on more than 80% of plays, as was the case in the two losses to Seattle and Purdy’s three-pick game against Carolina, things aren't going well. When it’s 75% or lower, the offense typically hums. Purdy was in the 'gun for just 74% of his dropbacks in that Week 1 win. It was also at 74% in the 2024 win, when the 49ers dropped 30 on Macdonald’s defense, before it reached its final form.

Based on how the 49ers are operating in 2026, Shanahan will want that number even lower on Sunday. The veteran play-caller has added a few new tricks, and most of them feature Purdy under center. 

Shanahan has really spruced up his running game, with new motions and alignments. It’s a nice blend of old-school looks with modern features. On this play, fullback Kyle Juszczyk motions into an old split-back look right as the ball is snapped, and then the 49ers run an old counter concept that could have been ripped out of Bill Walsh’s playbook.

Younger coaches like Bears Ben Johnson, Liam Coen, and Klayton Adams have pushed run-game creativity forward, and Shanahan isn’t falling behind. He could have been content with his A Million Different Ways to Run Outside Zone run game, which had always worked for him, but he knows smart defensive coordinators like Macdonald are always adapting.

Macdonald’s run defense has evolved since his first season in Seattle. The loss to San Francisco may have been one of the moments that spurred the change. The 49ers rushed for 228 yards and exposed some holes in the Seahawks' run front. Macdonald patched them up with run blitzes to close the gaps offenses were trying to attack. Here’s an example from the opener.

What looks like an inviting C-gap bubble before the snap…

… gets closed by a blitzing defensive back after it.

In 2024, Macdonald’s first season, Seattle called blitzes on 13% of run snaps, per Pro Football Focus. Last season, that number jumped to 23%, and it’s up to nearly 30% in 2026.

Sunday’s chess match between Shanahan and Macdonald will start in the trenches. The 49ers coach will look for soft spots up front to exploit with the run. Macdonald will try to hide those soft spots as best he can. It’s like a game of "Battleship" being played with 300-pound athletes instead of small plastic pieces.

If Shanahan can win that game within the game, Purdy should be at his best and primed for another monster game, solidifying his spot as the top candidate for MVP. More importantly, the 49ers would have carved out a two-game lead in the division and established themselves as the NFC’s best team.