motor trouble

[tgsx750f2000]

I have a 1999 yamaha 90 hp motor. This Saturday the alarm went off and the motor started running bad. It happened to me twice. The pisser was working the entire time. The first time I had been running it for awhile before it did it. The 2nd time we had been sitting for about a hour and i took off for about 400 yards and it did it again. Both times I killed the engine let it sit for just a couple minutes. When i would turn the key back on the alarm was still sounding. I cranked it and it was still running bad, but when I would give it gas the alarm went off and it started running good again. Any help would be appreciated.