The Alex Smith-49ers union will continue for at least another season.The agreement, first reported by the NFL Network's Michael Lombardi, came more than a week into the free-agent signing period and included an "ironing-out" session with coach Jim Harbaugh after Peyton Manning spurned the 49ers on Monday to sign with the Denver Broncos.But, in the end, Smith is back with the 49ers -- just as everyone around the NFL thought would happen all along.Smith's return to the 49ers had its share of drama, though. Harbaugh and offensive coordinator Greg Roman secretly traveled to Duke University in Durham, N.C., on March 13 to watch Manning throw."When the two of us started to talk, I very easily could have seen myself being a 49er," Manning said. "Thats why it was so hard."In the meantime, Smith took the first free-agent visit of his career on Sunday, meeting with Miami Dolphins coaches and team officials. But in the end, Smith decided -- despite some hard feelings -- that the 49ers offered him the best opportunity.Then, the 49ers waited for Manning to make a decision. And once Manning informed the 49ers of his decision, Smith found his old job waiting for him. Smith considered the 49ers' first and final contract proposal a low-ball offer."We have a contract on the table and it's up to him," 49ers CEO Jed York said on Monday. "We'd like for him (Alex Smith) to be here, and we'll see where it goes."Harbaugh was seen leaving the 49ers' team offices mid-day Monday, en route to a suspected meeting with Smith.Although not satisfied with the contract terms, Smith is back with the 49ers after enjoying his best NFL season under the direction of Harbaugh, Roman and quarterbacks coach Geep Chryst.The 49ers won the NFC West with a 13-3 record and reached the NFC championship game with Smith at quarterback.Smith's efficient play enabled the 49ers to tie the NFL record for fewest turnovers in a season with 10.He threw just five interceptions, and finished the season with 159 consecutive regular-season pass attempts without getting picked off. Steve Young holds the 49ers' record with 183 attempts without an interception, 1993.In two playoff games, Smith attempted another 68 passes without throwing an interception.Smith's best performance of the season came in the playoffs when he led the 49ers on two late-fourth quarter touchdown drives in a remarkable 36-32 victory over the New Orleans Saints in an NFC divisional-round game at Candlestick Park.It was the sixth time Smith led the 49ers to a fourth-quarter comeback victory on the season. Four of those come-from-behind wins took place on the road, tying the franchise record that Joe Montana set in 1989.While the 49ers' passing game was efficient with Smith, it was far from prolific. The 49ers ranked 29th in the league in passing yards. Moreover, the 49ers ranked 31st in third-down conversions (29.4 percent) and 30th in red-zone efficiency, scoring touchdowns on just 40.7 percent of their trips inside the opponents' 20-yard line.But the sides did not immediately hammer out a contract extension because the 49ers were reluctant to make a commitment in years and money that would lock him in as the starter for multiple seasons.The 49ers traded up to the No. 36 overall spot in the 2011 draft to choose Colin Kaepernick, and the 49ers wanted to keep the door open for Kaepernick to take over the starting job from Smith.Kaepernick has been working out daily at the 49ers' practice facility. On Monday, Kaepernick declined comment, saying only that he's "just working."Harbaugh believes in creating competition at all positions. And Kaepernick appears to have an opportunity to convince the coaching staff at some point in the near future that he gives the 49ers their best chance at success.Smith arrived with the 49ers in 2005 as the No. 1 overall pick. He signed a six-year, 49.5 million contract. But Smith agreed to a sizable pay cut after his fourth season. He ended up collecting 31.5 million in his first six seasons.Following the 2010 season, Smith admittedly was set to finally leave the 49ers. But soon after Harbaugh was hired to a five-year, 25 million contract, the new coach convinced Smith to stick around.During the NFL lockout, Smith took on a leadership role as he organized the "Camp Alex" workouts at San Jose State, though he was not officially under contract. The day the lockout lifted, Smith signed a one-year, 4 million contract. He maxed out his incentive package with another 2.5 million.Smith posted the best season of his career with a 61.4 completion rate, 3,144 yards passing with 17 touchdowns and five interceptions, and a passer rating of 90.7.
Selection: Third round, No. 104 overall
SANTA CLARA -- The 49ers traded back into the end of the third round to select a quarterback to join Brian Hoyer and Matt Barkley on the 49ers' roster.
General manager John Lynch's fourth trade of the draft netted the team the grandson of legendary NFL personnel man Bobby Beathard. His grandson, C.J., joins the 49ers after a four-year career at Iowa. Beathard completed 58.6 percent of his passes last season with 17 touchdowns and 10 interceptions.
Coach Kyle Shanahan believed Beathard was the best fit for his offense, and Beathard said he was excited about learning the 49ers' offensive scheme.
“I think I’ll fit in very well," Beathard said on a conference call with Bay Area reporters. "I come from a background, a football background, so I know a lot about coaches and things like that. And I have a lot of, you know my grandpa and uncles have a lot of great things to say about coach Shanahan.
"And having watched his schemes and offensive philosophy and style, I think I’ll fit in very well with that. And I’m just looking forward to getting there and practicing and getting ready to work.”
Beathard was not generally expected to be chosen within the first two days of the draft. He was the sixth quarterback selected, falling behind Mitch Trubisky, Patrick Mahomes, Deshaun Watson, Deshone Kizer and Davis Webb.
"I’m just thankful the 49ers and coach Shanahan’s staff you know, saw the potential in me and they believe in me enough to give me this opportunity. And like I told them, they won’t regret it," Beathard said.
The 49ers traded up with the Minnesota Vikings. The Vikings had the No. 104 pick, and called the 49ers to see if they were interested in a trade. After some consideration, the 49ers decided to move up from No. 109 while also giving the Vikings a seventh-round pick at No. 219.
Beathard was chosen before any of the draft prognosticators had him being selected.
"I don’t really pay attention to the mock drafts very much," Beathard said. "I had a lot of communication with various teams. I’m confident in my abilities and you know I’m just thankful the 49ers and coach Shanahan’s staff saw the potential in me and they believe in me enough to give me this opportunity. And like I told them, they won’t regret it.”
Shanahan said the 49ers "had an idea" Beathard would be selected in the fourth round. The 49ers were certainly going to pick him in the fourth round, but they moved up to the end of the third round just to be able to have a good night of sleep.
"Might he have been there at 109? That’s what we had to weigh," Lynch said. "But at the end of the day, we felt like it was worth it to be able to go to bed knowing that we had a player that we liked and want the opportunity develop at the quarterback position."
And that's what Shanahan plans on doing. He said Beathard is not coming to the team this season to compete with Hoyer for the starting job.
"We’re bringing him in here to develop him and give him a chance, but just like any other position, everyone competes," Shanahan said. "Brian is our starting quarterback and, right now, Matt Barkley is our second. And I look at him to come in and be our third with us only having three on the roster.
"By no means did we come into this draft thinking we’re going to get a guy to compete with Brian."
Shanahan said Beathard and Pitt quarterback Nathan Peterman were the two quarterbacks in the draft who ran offenses in college most similar to the offense he is installing with the 49ers.
"One thing that helps is being able to see guys play the way you’re going to ask them to play," Shanahan said. "It helps being at Iowa and watching the system he’s in. It’s easier to see to watch him over the years. He’s a three-year starter. He’s led his team to a bunch of wins, especially in 2015 when they had a better team and he played unbelievable."
As a junior at Iowa, Beathard completed 61.6 percent of his pass attempts for 2,809 yards with 17 touchdowns and five interceptions.
"He’s a leader. He’s tough. He processes very well," Shanahan said. "He's extremely accurate and he lives and dies football."
Height: 6-2 3/4
Selection: Third round, No. 66 overall
SANTA CLARA – The 49ers selected Colorado cornerback Ahkello Witherspoon, a Sacramento native, in the third round of the NFL draft with the No. 66 overall pick.
“Being close to home is an incredible opportunity, as well as the type of defense they play -- press man, up in your face,” Witherspoon said. “When I came in for a visit, they were asking me if I’ve adopted that role and if I’d be willing to continue that. And I said, ‘Absolutely.’
“It’s an opportunity to play for such a great organization, close to home, with such a savvy defensive mentality. I think it’s going to be a great place for me.”
The 49ers were also scheduled to have the next pick, but traded the selection at No. 67 for the New Orleans Saints’ second-round pick in next year’s draft, as well as a seventh-round selection (No. 229 overall) this year. The 49ers now have 10 picks in next year’s draft.
The Saints used that pick at No. 67 to select Tennessee running back Alvin Kamara.
Witherspoon began his college career at Sacramento City. He played his final three college seasons at Colorado. He started 12 games last season and earned second-team All-Pac-12 honors.
Witherspoon led the nation with 22 pass breakups. He recorded one interception -- a game-saving pick in the end zone to preserve a 41-38 victory over Oregon. A pre-med student majoring in ecology and evolutionary biology, he said he aspires to be a doctor after his football career.
But Witherspoon said he is committed to football and promised the 49ers during his visit to Santa Clara that he will make huge strides over the next few years as he continues to develop as a player.