Toadbert appears to be on very good terms with Mario Bros. as seen by the help that he had provided for them throughout the series (from providing them with hints to almost fighting alongside them in a battle against Sunnycide).
He first appears at Princess Peach's Castle where he along with Mario, Luigi, Peach, Toadsworth and several other Toads were discussing about the Blorbs, a recent disease in the Mushroom Kingdom that was causing the Toads to inflate many times their size and roll around uncomfortably. However just as their discussion was getting stronger, Bowser soon arrives to kidnap the princess (thus disturbing their conference). Fortunately, Mario was there to defeat him. Peach soon uses her powers to send Bowser flying out of the castle.
Unfortunately, Bowser's apperance had scared away most of the members, leaving only Toadbert, Mario, Peach, Starlow, Toadsworth and a sleeping Luigi to be the only members present. The group soon starts to get discouraged about what to do with Toadbert even suggesting to stop the meeting. Toadsworth however refuses and suggests for the group to go find the other members. Unfortunately, their plan was interrupted once again as Bowser re-enters the castle. Toadbert along with the other heroes were soon sucked into Bowser's body at the helpless moment and they were soon all separated from each other.
After being found and freed from a closed-in area in Bowser's body, Toadbert helps the Mario Bros. by scouting out areas of Bowser's body and often appears to instruct the brothers about the functions the various areas of Bowser's body. He also has a hint booth in Toad Square, a location in Bowser's body where most of the Toads that were sucked into his body can be found. He also appears to be in good terms with Toadsworth as the two can be seen accompanying the bros. in several areas throughout Bowser's body.
In the ending of the game (when everyone is out of Bowser's body), Toadbert along with Mario, Luigi, Starlow, Peach, Toadsworth and several other Toads can be seen celebrating happily in front of a confused yet furious Bowser. When Bowser discovers that Mario, Luigi and the others were inside his body the whole time (with the added discovery of finding out that "Chippy", his guide and minion who he trusted for the adventure was actually Starlow), he releases his anger in a violent way by breathing out fire causing most of the Toads (including Toadbert) to flee. Eventually Bowser's anger leads up to the final battle of the game (shown as cutscenes) where he fights the Mario bros..