He spent ten of his seasons in the AFL with the SaberCats; over this span, he won four ArenaBowl championships and three Defensive Player of the Year (DPOY) awards.
Thomas also started the Sugar Bowl for Florida State, recording five tackles; his efforts helped the Seminoles defeat Virginia Tech, 46–29, to win a National Championship.
The following year, the team again advanced to the National Championship Game; while Thomas was again a starter, Florida State lost to the Oklahoma Sooners by a score of 13–2.
The SaberCats would then win two playoff games to reach ArenaBowl XVI; there, they crushed the rival Arizona Rattlers in a 52–14 rout to capture the first championship in franchise history.
Despite this setback, Thomas collected his second championship (while on the injured reserve) when the SaberCats defeated the Rattlers in ArenaBowl XVIII.
In 2005, Thomas returned to action; while he played well (recording 49.5 tackles, 10 pass breakups, and 5 interceptions in 13 games), he failed to replicate the dominance of his first two seasons.
He contributed 78.5 tackles (69 solo), 20 pass breakups, and 9 interceptions (two of which were returned for touchdowns); his fantastic play helped the SaberCats to a 13–3 regular season finish.
His dominance helped the SaberCats reach the playoffs for the ninth consecutive season; they ultimately advanced to ArenaBowl XXII, which they lost (59–56) to the Philadelphia Soul.
By 2012, despite the lack of a formal announcement, it appeared that he had entered retirement; in light of this, he was elected to the Arena Football Hall of Fame.
Thomas' resurgence helped the SaberCats to a 13–5 finish; they lost to the defending champion Arizona Rattlers in the first round of the playoffs.
While his numbers dropped considerably from his 2013 campaign, he remained one of the league's best cornerbacks; in 2014, Thomas tallied 70.5 tackles (60 solo), 14 pass breakups, and 8 interceptions (one of which was returned for a touchdown) in a career-high 18 games.
Thomas remained a key part of the SaberCats' top-ranked defense; despite this, he failed to garner any major awards in 2014.
During the offseason, San Jose had acquired AFL superstar cornerback Virgil Gray; this served to bolster the belief that Thomas' career had reached its end.
During a Week 3 contest against the Tampa Bay Storm, Gray suffered a season-ending knee injury; days later, the SaberCats announced Thomas' return to the team.
During the game, Thomas recovered a Michael Lindsay fumble deep in Jacksonville territory; the turnover resulted, shortly thereafter, in a key score for the SaberCats.
He has been a part of all four of the SaberCats' ArenaBowl championship teams (XVI, XVIII, XXI, and XXVIII); he is the only person to have won all four as a player.