The changing 49ers QB outlook

Shanahan and Lynch went from passing on QB answer in their first draft — one that saw the 49ers trade down from No. 2 to No. 3 and pass on Patrick Mahomes, Deshaun Watson (and Mitch Trubisky, who went second overall) for since-departed defensive lineman Solomon Thomas — before seeing a long-term starter fall into their laps at that year’s trade deadline. That October 2017 trade, which cost the 49ers a second-round pick (No. 43 overall), is still paying dividends five years later.

The Garoppolo era appears near an end, but the 49ers are suddenly all-in again on a player who spent the offseason, training camp and preseason away from the team. Trey Lance‘s season-ending ankle injury dealt an inexperienced prospect a tough blow, but the Week 2 setback — albeit awkwardly — may have bolstered one of the NFL’s top rosters. Garoppolo’s re-emergence figures to stabilize the 49ers, providing them perhaps a considerably elevated floor. (An early-season Lance benching was already being rumored.) Instances in which a contending team loses a QB1 and is viewed as better for it are not exactly common throughout NFL history; this could be one of the few.

This reality nearly fell apart months ago, as the 49ers came close to trading Garoppolo before his value-hijacking March shoulder surgery. The Browns, Rams and Seahawks later loomed as a destinations in the event the 49ers cut him — this saga’s expected endgame in its final weeks. Although the 49ers have said the plan all along was to trade their four-plus-year starter, he always loomed as unusual Lance insurance. The 49ers drafted one of the most atypical quarterback prospects in league history last year, and the Division I-FCS product’s inexperience made going into the season without Garoppolo a tremendous risk. Yet, that appeared the plan. Lynch’s suggestion to approach Garoppolo with a pay-cut proposal ended up preventing one of the NFC favorites from seeing Lance’s injury leave them with an untenable in-house starter option.

While Garoppolo gives Shanahan a safer option to lead a three-All-Pro offense, the 49ers are in one of the weirder places at quarterback in recent memory. Their No. 3 overall pick will have finished his first two seasons with four starts and 102 pass attempts. Those numbers are not unprecedented by any means, but this is obviously a different situation compared to the likes of Jordan Love or busts Johnny Manziel (eight starts through two seasons) and Paxton Lynch (four). Lance, who could be kept through 2025 via the fifth-year option, remains firmly in San Francisco’s plans. But this rehab year will nix another shot at in-game development. These chances have continually been taken away from the North Dakota State alum.

Entering 2023, Lance will have just one season of regular starter work on his post-high school resume. After redshirting in 2018, Lance tore up the FCS level (albeit with that tier’s best program) with 28 touchdown passes and no interceptions and led the Bison to another national championship. The COVID-19 pandemic led most of college football, save for Division I-FBS, to cancel its 2020 seasons (for the fall, at least). After a one-game 2020, Lance declared for the draft. Despite a highlight reel consisting entirely of redshirt-freshman plays, the dual-threat talent managed to follow fellow Bison standout Carson Wentz by becoming a top-three draftee. But Lance suffered a finger injury in 2021, limiting him during a season in which he was not viewed as a Garoppolo threat.

A sought-after QB prospect having thrown 420 passes in five seasons since high school is historically unusual territory for a player still expected to be a long-term NFL starter. Lance’s misfortune comes after an inconsistent preseason, one that helped push the 49ers to solidify a Garoppolo recommitment. A rocky Week 1 start on a waterlogged Soldier Field enhanced the mystery surrounding Lance’s status. A high ceiling may remain, but after four years away from full-time duty, can the 49ers be sure? San Francisco is also now veering toward Green Bay-Love territory; the 49ers will have gotten next to nothing from a first-round QB contract through two years. Though, Garoppolo’s restructure gives the team some flexibility the Packers lack thanks to Aaron Rodgers‘ record-setting $50.3M-per-year extension.

Fielding an NFC championship-qualifying team with scant contributions from a No. 3 overall pick highlights the 49ers’ roster strength. Last year’s success and this year’s largely Lance-less operation also magnify the franchise’s decision to trade two future first-round picks to move up nine spots for such an unproven commodity. The 49ers have won in spite of their 2021 Lance- (or Mac Jones?)-motivated decision. It is understandable the 49ers dealt into future draft arsenals to land a quarterback upgrade, as Garoppolo (12th- and 13th-place QBR figures in 2019 and ’21, respectively) maxes out as an above-average option. But the team made a luxury pick with a Super Bowl-caliber roster in place.

The Shanahan-Jones connection likely will not fade anytime soon. Although Jones was not viewed on Lance’s level as a prospect last year, the 49ers’ April trade was initially believed to be for the Alabama QB. The 49ers went through an extensive investigation into Jones, the eventual Patriots pick at No. 15, before deciding on Lance. A report indicating the 49ers, who had held 2021’s No. 12 overall selection, being worried about the Patriots leapfrogging them for Jones does point to the less mobile passer being their initial preference. While Shanahan said both Lance and Jones would have been good options, the Jones what-if could linger.

Lance’s injury also thrusts Garoppolo’s health history back to the forefront. In addition to the shoulder malady that sidetracked his trade market, the ninth-year vet played through calf and thumb issues in 2021, went down with a season-ending ankle problem in 2020 and missed most of the ’18 season due to an ACL tear. The 49ers having 2022 Mr. Irrelevant Brock Purdy and practice squad journeyman Kurt Benkert as Garoppolo’s only backups suddenly becomes a concern. Shanahan’s intermittent success with a rookie UDFA (Nick Mullens) notwithstanding, the team turning back to the trade market — this time to supplement Garoppolo — would make sense.

A backup with multiple years of control could be a priority as well. Garoppolo’s 2018 extension expires in March. The 49ers venturing to two NFC title games in three seasons without a high-end quarterback represents an achievement when considering the position’s rise in stature as rule changes have pushed most teams to build around the passing game. The quarterback that drew scrutiny for holding his team back being viewed as a rejuvenation tool is ironic, but the 49ers did well to forge this compromise. It could go down as a seminal compromise.

But little is settled for the team beyond 2022. After Garoppolo makes another push at a Super Bowl championship, his restructure’s no-franchise tag clause would stand to lead him to free agent market unlikely to include many attractive options (Lamar Jackson is not hitting the market, and Year 23 might actually be it for Brady). At that point, the paused Lance era will return to the 49ers’ front burner. Lance’s uncertain trajectory will be appropriate for a team that has seen its QB situation produce a highly unpredictable contender during the Shanahan-Lynch period.