In 2000, the Nets hired as the team president Rod Thorn, who was best known for being the Bulls General Manager who drafted Michael Jordan and an executive with the NBA. Immediately, he began to assemble the components of the most talented team since the ABA champions of the mid-1970s. With the first pick in the 2000 Draft, the Nets selected Kenyon Martin from the University of Cincinnati. On the night of the 2001 Draft, the Nets traded the rights to their first round selection (Eddie Griffin) to the Houston Rockets for their draft selections -- Richard Jefferson, Jason Collins and Brandon Armstrong.

Just after the 2001 draft, Thorn made his boldest move. He traded all-star Marbury to the Phoenix Suns for another all-star point guard Jason Kidd. The move gave the team something it had been lacking for practically its entire NBA existence, a floor leader who also made his teammates better.

That next season the Nets had their best season in their NBA history. The team won its first Atlantic Division title, finishing the regular season at 52-30 and were seeded first in Eastern Conference and faced Indiana in the first round of the 2002 NBA Playoffs.

After losing the first game at home, the Nets then went on to win the next two games, before losing game four on the road. In front of a sellout crowd, the Nets played one of the more memorable games in NBA Playoff history in game five. The Nets led by nine points with five minutes remaining in regulation, however Reggie Miller made a 35-foot 3-pointer at the buzzer to send the game into overtime (It should be noted that replays later showed that Miller's shot was actually after the buzzer and shouldn't have counted). After Miller sent the game into a second overtime with a driving dunk, the Nets pulled away for a 120-109 double-overtime victory.

In the Eastern Conference Semifinals, they defeated the Charlotte Hornets four games to one to advance to the Eastern Conference Championship for the first time facing the Boston Celtics. After winning game one versus the Celtics, the Nets lost game two at home. In game three, the Nets led by 21 points going into the final period, but a tremendous Celtic comeback gave the Celtics a 94-90 victory and a 2-1 series lead. In game four played on Memorial Day afternoon in Boston, the Nets led most of the way but once again the Celtics found a way to tie the game with a minute remaining. However, in this game the Nets made enough plays at the end of the game to win it - Harris made two free throws with 6.6 seconds left and when Paul Pierce missed two free throws that would have tied the game with 1 second left, the series was tied at two games each. In game five, the Nets went on a 20-1 run early in the fourth period to coast to a 103-92 victory and a 3-2 lead in the series. In game 6, the Nets trailed by 10 at halftime, but rallied in the second half to take the lead. Van Horn's three pointer off a Kittles pass with 50 seconds left in the game clinched the Nets first Eastern Conference Championship, four games to two.

In the 2002 NBA Finals, the Nets were swept by Shaquille O'Neal, Kobe Bryant and the Los Angeles Lakers in four games.

Before the 2002-03 season, the Nets traded Van Horn to obtain Dikembe Mutombo from the 76ers. The move to improve the team did not work out as Mutombo sat out most of the season with a wrist injury. Despite Mutombo's absence, the Nets finished with a 49-33 record and repeated as Atlantic Division champs. In the 2003 NBA Playoffs, the Nets won their second consecutive Eastern Conference championship. The defeated the Bucks in the first round of the playoffs four games to two, then swept the Celtics and Pistons in consecutive series to advance to the 2003 NBA Finals, this time facing the Western Conference champions San Antonio Spurs. The Nets and Spurs split the first four games in the series, but the Nets played erratically in a Game 5 loss at home to go down in the series three games to two. In Game 6, the Nets led the Spurs by 10 points on the road with 10 minutes remaining, but the Spurs went on a 19-0 run to take the title in six games.

Following the 2003 Finals, Kidd became a free agent and the Spurs pursued signing him away from the Nets. However, Kidd re-signed with the Nets, along with center Alonzo Mourning.

In 2004, The Nets Again won the Atlantic Division Title, however their run of conference championships was halted in the Eastern Conference Semifinals by the eventual NBA Champion Detroit Pistons. The Nets stole Game 5 In Detroit in Triple Overtime, only to blow a huge lead early in Game 6 in New Jersey. The Pistons won Game 7 in a Rout and took the series 4 Games to 3. Notably, Jason Kidd was held scoreless in Game Sevem.

In 2005, after two disappointing seasons, the Nets acquired disgruntled star Vince Carter from the Toronto Raptors in exchange for Alonzo Mourning. Mourning was then released and signed with Miami. Teamed with Kidd, Carter rallied the team from being more than 10 games out of the playoffs to gain the final seed in the Eastern Conference. However, the duo could not overcome O'Neal again and were swept by the Miami Heat in the 2005 postseason.

During the summer of 2005, the Nets actively pursued a starting-quality power forward to fill that void after drafting Antione Wright, a 6-7 swingman because all the talented powerforwards were taken in the draft. Eventually settling on Shareef Abdur-Rahim, they actively courted him and gained his approval even though they could only offer him the mid-level exception. In order to get him a larger, more lucrative contract, the Nets pursued a sign-and-trade with Portland. There, negotiations hit a snag because Portland demanded a First-round draft pick, which the Nets adamantly refused to part with. Eventually, the nets agreed to give Portland a protected first-round pick and their trade exception acquired from the Kerry Kittles trade. This allowed the Nets to keep their midlevel exception for signing other players. They used part of it to resign Cliff Robinson for 2 years in response to Brian Scalabine's departure. They actively courted Keyon Dooling before he signed with Orlando. They then turned their attention to a different backup to Kidd, and eventually signed talented, but aggravating (at times) Jeff McInnis.