Things were even better for the Phantoms in 1998, as they improved their regular season performance for the second straight year, finishing with a 10–6–2 records and 2nd in the Northeast behind Rhode Island Stingrays.

New Hampshire faced the Chicago Stingers in the Championship Game, but fell 3–2 in another overtime classic, and eventually finished the year as the second-best team in the D3 Pro League.

Fortunately, the Phantoms won the game 3–2 with a golden goal from Ebbie Kodiat, and progressed to the third round – where they were unceremoniously dumped out of the competition 4–1 by A-League side Rochester Raging Rhinos.

2004 brought the first piece of silverware to New Hampshire when, after eight years of competition, they topped the Northern Division standings, four points clear of second placed Westchester Flames.

The Phantoms got a bye to the Pro Soccer League playoff semi finals, and were well-placed to make their second trip to the Championship game, but were unexpectedly beaten 1–0 by Southern Division winners Charlotte Eagles, and went home early.

A 6–0 hammering of the Northern Virginia Royals at home in early June that featured a brace from striker Mark Manganello briefly raised the spirits, and back-to-back wins over Long Island Rough Riders and Charlotte Eagles hinted that a late-season surge could be on the cards in Manchester, but the Phantoms reverted to their poor form quickly.

The Phantoms even enjoyed a brief run to the third round of the US Open Cup, taking out Connecticut-based USASA side Milford International before being walloped 5–1 by USL First Division outfit Rochester Raging Rhinos.

They also suffered some humiliating defeats during this stretch: Western Mass Pioneers hit them for six in mid-July, and put another half dozen past them in a 6–2 win in August.

The Harrisburg City Islanders hit four in a bad-tempered game which saw three men sent off in injury time, and the Richmond Kickers showed no mercy to goalkeeper T.J. Tomasso when completing an 8–0 rout on the final day of the season.

The Phantoms did manage to pick up two more wins – 2–1 over Richmond Kickers and a hard-fought 3–2 over Wilmington Hammerheads – but were eliminated from playoff contention well before their 3–1 loss to Cincinnati on the final day of the season.

In an attempt to consolidate their finances and restructure their organization, the Phantoms took voluntary relegation from the USL Second Division to the Premier Development League at the end of 2007.