They made it to the national semi-finals, beating Grand Rapids Explosion, Kalamazoo Kingdom and Des Moines Menace before eventually falling 2–0 to the Central Coast Roadrunners in the final four.

The Bucks also made their debut in the US Open Cup with a 3–2 victory over USISL D3 Pro League side Wilmington Hammerheads, before losing to the A-League's Rochester Ragin' Rhinos in the second round.

The Bucks won the Great Lakes division of the newly renamed PDL in 1999, but lost 2–1 to Sioux City Breeze in the Conference Semifinals.

They also reached the third round of the US Open Cup, after defeating the Austin Lone Stars and Minnesota Thunder, but were eliminated by the Tampa Bay Mutiny of the MLS.

They won 3–0 over Maryland-based amateur side Jerry D's, and defeated MLS's New England Revolution 1–0, with Chad Schomaker scoring the winning goal in the 90th minute, before losing their next game on penalty kicks to Miami Fusion after a 3–3 draw in regulation time.

The Bucks missed the playoffs for the first time in 2001, beaten into third place in the Great Lakes Division by Chicago Fire Reserves and West Michigan Edge, but did manage to progress to the second round of the US Open Cup for the third year in a row, knocking out amateur side Chaldean Arsenal before losing to the New England Revolution 7–1.

In the US Open Cup, the Bucks beat USL Pro Select League Long Island Rough Riders, before losing 4–0 to the New York/New Jersey Metrostars in Round 3.

Paul Snape, who had played for the team for many years, was appointed head coach in 2005, but the first few games of his tenure were rocky: three consecutive wins were followed by a four-game winless streak.

After defeating the St. Louis Lions in the playoff semi-final, the Bucks retained their Conference title with a 3–0 win over Chicago Fire Premier, returning to the national stage for a second consecutive year.

A penalty shootout victory over Brooklyn Knights after a 1–1 tie in the semi-finals sent the Bucks to the Championship game for the second consecutive year where they once again played against Southern Conference champions Laredo Heat.

His replacement, Ian Daniel, had his kick saved by Laredo goalkeeper Ryan Cooper; teenager Felix Garcia then scored the winner for the Texans.

They received a berth in the US Open Cup for the third straight year, but fell in the first round against USL League 2 side Cleveland City Stars.

Despite a strong regular season, they were eliminated in the first round of the playoffs by Kalamazoo Outrage, who scored an 86th-minute equalizer to force extra time, and ended the game at 3–1.

[6] On match days, the River Rats gather at Soggy Bottom Bar for a pre-game provocation before marching a half-mile through Carriage Town to the Atwood Stadium turnstiles.