The 49ers locked down Jimmy Garoppolo as their franchise quarterback. Now what?

The San Francisco 49ers’ turnaround started at the cost of a 2018 second-round pick. It’s going to cost hundreds of millions of dollars to continue.

General manager John Lynch’s reclamation project in Santa Clara took another step forward Thursday when he signed quarterback Jimmy Garoppolo to a five-year, $137.5 million deal that will make him the league’s highest-paid player. The contract includes $74 million in guarantees.

That’s a lot of money for a player who has made only seven starts in his four-year NFL career, but Garoppolo is a worthy investment. He’s won all seven of those games, an especially impressive feat given his 2017 setting. The 49ers had gone 0-8 before trading for Garoppolo and were 1-10 when they decided to start him. They finished the season 6-10 with wins over three playoff teams — the Titans, the Rams, and the Jaguars.

That answers the biggest question Lynch faced when he took his position as the team’s top executive. San Francisco went into the 2017 offseason with zero quarterbacks under contract. With Thursday’s news, he’ll have a rising star taking snaps through 2022.

But there’s still plenty of work to be done. The 49ers went 3-24 over the last two seasons before Garoppolo took over. As impressive as his 5-0 run behind center was, he’ll need an upgraded roster to avoid regression in 2018.

So how will the 49ers spend the ~$90 million in cap space they’ll have?

Garoppolo was an expensive necessity in a league that’s proved the value of elite quarterbacks time after time. He was also one a frugal San Francisco front office could afford. Before the signing, the team had a projected $117 million in salary cap space to spend in 2018, per Spotrac — more than any other team in the NFL and more than three times the league’s average.

We don’t know the structure of Garoppolo’s deal, and it’s tough to use former “highest-paid player” deals like the ones given to quarterbacks like Derek Carr and Andrew Luck as a template because they were extensions while Garoppolo was headed for free agency. Let’s assume the first year of the deal tacks on an above-average cap hit to take advantage of the team’s space and leave breathing room for the future. Even if that number is $30 million, that still leaves the franchise with approximately $87 million to spend — more than any team but the Browns.

So where will Lynch spend that money? Major upgrades need to be made on each side of the ball. The first step will be reconfiguring a passing defense that has to face Russell Wilson and Jared Goff four times each season. Last year’s Niners ranked 25th or lower in the NFL in the following categories:

• sack percentage
• scoring defense
• red-zone defense
• opponent yards per pass

Improving the pass rush should be a top priority

While the club has invested high draft picks on bolstering its defensive front, it has yet to pay off in the pass rush. Elvis Dumervil, a 33-year-old free agent pickup, led the team with 6.5 sacks while former first-round choices Solomon Thomas, DeForest Buckner, and Arik Armstead combined for 7.5. There’s a lot of talent in that trio, which helps provide the basis of a stout run defense. But they’ll have to create more pressure to make life easier for a young, oft-injured, and underperforming secondary.

Reeling in a top-flight pass rusher is an expensive prospect. Calais Campbell only left Arizona after securing $15 million per year and $30 million in guarantees from the Jaguars. In 2018, players like Ziggy Ansah and Demarcus Lawrence will fill that role as well-compensated defensive ends (though they both could end up getting the franchise tag).

Lynch doesn’t necessarily need to pay a prohibitively expensive quarterback crusher yet. Buckner and Thomas were both reliable pass rushers in college who still have time to develop as they head into their third and second years in the NFL, respectively. Lynch would still be smart to chase some veteran talent who can add more punch up front, even if it means overspending on short-term deals. Players who fit that bill include Adrian Clayborn, Alex Okafor, Connor Barwin, or Lamarr Houston.

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The secondary needs a lot more work

It will take more work to overhaul an overtaxed secondary. The 49ers will have to hope safeties Jimmie Ward and Jaquiski Tartt are ready to be the foundation of the franchise’s last line of defense, as Eric Reid seems destined to depart as a free agent. Those two combined for only 16 games in 2017, so some of the team’s defensive deficiencies can be explained by their frequent absences.

Things are less certain at cornerback. Rookie third-round pick Ahkello Witherspoon and former backup Dontae Johnson each suffered through growing pains in a season where Blake Bortles, of all people, was able to hang 380 passing yards on them (albeit at the cost of throwing three interceptions).

Johnson is a free agent this spring, and while K’Waun Williams was a useful slot corner, he may not be able to translate that skill to a full-time role on the outside. There’s room for an upgrade here, and there will be several useful cornerbacks available both in the draft and in free agency. SB Nation’s Dan Kadar has them selecting Ohio State corner Denzel Ward, but the Niners may not stop there.

Lynch already spent big to give one former New England Patriot a chance to shine, so why not another? Malcolm Butler’s days in Foxborough are likely over, and he’d fill several of San Francisco’s needs in 2018. Other established players like Trumaine Johnson and injury risks like Kyle Fuller and Morris Claiborne would be fits as well, assuming their teams don’t lock them down before they can hit the free agent market in earnest.

Lynch will also have to spend money to protect his $137.5 million investment

San Francisco’s quarterbacks were sacked on only 6.6 percent of their dropbacks, a relatively middling rate. A closer look shows those passers dealt with much more pressure than the numbers suggest. 49ers quarterbacks were hit 116 times last season — more than all but four teams in the league. That’s a stark reminder of the pocket-collapsing pressure Garoppolo had to face as his season wore on.

Protecting him would be paramount to the team’s success, as last year’s 1-10/5-0 splits prove. Upgrading a unit Football Outsiders ranked as 18th-best in pass blocking will certainly be on Lynch’s to-do list. Left tackle Joe Staley put together a typical Pro Bowl season, but at age 33 his play could begin to decline next fall.

The rest of the line — Laken Tomlinson, Trenton Brown, Brandon Fusco, and Daniel Kilgore — was effective in the running game but below average when it came to protecting its quarterbacks. Fusco and Kilgore are each free agents this spring, and their departure could create space for upgrades in the middle of the line.

Unfortunately for Lynch, there isn’t a flush market of potential free agents for 2018. Nate Solder is arguably the best blocker set to be available, and he plays the same position as Staley. Bigger names like Luke Joeckel, Greg Robinson, and Jonathan Cooper have failed to live up to expectations in brief, disappointing NFL careers. Instead, the 49ers may have to bet on a steady, lesser-known project like the Jets’ Wesley Johnson, the Broncos’ Billy Turner, or the Chiefs’ Zach Fulton.

What about the guys who Garoppolo will be targeting?

And then there’s the matter of surrounding Garoppolo with talent at the skill positions. Lynch proved he’s not afraid to pay for steady proven production on offense after handing out $68.5 million in contracts to wideout Pierre Garcon and fullback Kyle Juszczyk last offseason. He’ll have to open up the checkbook once more to restock a depth chart filled with anonymous players.

Garcon played well despite missing eight games due to injury, and former track star Marquise Goodwin proved himself as a legitimate NFL deep threat while gaining more than 17 yards per catch. There’s a significant roster falloff after them, however, creating a need for a true No. 1 wideout to take the reins in Santa Clara.

Lynch can take two paths to find that player in free agency — and one tacks on a ton of risk. The 2018 offseason is loaded with playmakers who bring plenty of baggage along with the kind of talent that can carry a team. Can Sammy Watkins stay healthy enough to live up to his contract? Which Terrelle Pryor are you paying for — the one who overachieved with the Browns or the one who sputtered out in Washington? Allen Robinson was an All-Pro with the Jaguars but is coming off a torn ACL that cost him his 2017.

That leaves Jarvis Landry, who led the league in receptions in 2017, as the surest thing in a volatile wide receiver market. With a similar build as Garcon, he could be the veteran’s heir apparent in San Francisco, though it would be expensive to lure him west. If Lynch can’t land a potential No. 1 WR this offseason, expect him to take a swing at a deep class of backup options that includes players like Marqise Lee, Paul Richardson, Donte Moncrief, and Jordan Matthews.

Lynch will also have to figure out what to do with starting tailback Carlos Hyde, who is a free agent. Hyde is a bruising runner who can punish defenses, but he also saw his efficiency take a hit last fall as his yards per carry dropped from 4.6 to 3.9. It may be time to move on from him and hand the reins to Matt Breida, who was effective as the rookie lightning to Hyde’s thunder in the backfield. If Hyde doesn’t re-sign, the team could gamble on his replacement either in the draft or through the market.

Keeping Garoppolo happy is about more than money — and now Lynch has to prove it

Garoppolo thrived with a team that had won just 11 percent of its games the two seasons before he became starter. That’s a great start, but not a sustainable one. With a quarterback locked down and a team on the rise, there’s no reason for Lynch not to spend in an effort to end San Francisco’s playoff drought at four years.

That doesn’t mean spending recklessly, however. Lynch raised some eyebrows by resetting the previously low-key fullback market with his $21 million deal for Juszczyk and guaranteeing a 30-year-old wideout $20 million, but those moves belied his team-building philosophy. He wants productive, low-risk veterans and understands he’ll have to pay a premium until his team starts winning.

That will be easier after last year’s 5-0 finish and the promise Garoppolo will be under center. Lynch has more flexibility to make moves this season than he did the year prior, but he’ll also face significantly greater expectations. The 49ers’ 2018 will be all about building a future around their new franchise quarterback. With a few shrewd signings, Lynch can ensure that future comes more quickly than anyone could have hoped.