We present simultaneous and continuous observations of the Hα, Hβ, He I D3, Na I D1, D2 doublet and the Ca II H & K lines for the RS CVn system HR 1099. The spectroscopic observations were obtained during the MUSICOS 1998 campaign involving several observatories and instruments, both echelle and long-slit spectrographs. During this campaign, HR 1099 was observed almost continuously for more than 8 orbits of 2.8 deg. Two large optical flares were observed, both showing an increase in the emission of Hα, Ca II H & K, Hβ and He I D3 and a strong filling-in of the Na I D1, D2 doublet. Contemporary photometric observations were carried out with the robotic telescopes APT-80 of Catania and Phoenix-25 of Fairborn Observatories. Maps of the distribution of the spotted regions on the photosphere of the binary components were derived using the Maximum Entropy and Tikhonov photometric regularization criteria. Rotational modulation was observed in Hα and He I D3 in anti-correlation with the photometric light curves. Both flares occurred at the same binary phase (0.85), suggesting that these events took place in the same active region. Simultaneous X-ray observations, performed by ASM on board RXTE, show several flare-like events, some of which correlate well with the observed optical flares. Rotational modulation in the X-ray light curve has been detected with minimum flux when the less active G5 V star was in front. A possible periodicity in the X-ray flare-like events was also found. Based on observations obtained during the MUSICOS 98 MUlti-SIte COntinuous Spectroscopic campaign from Observatoire de Haute-Provence, France, Kitt Peak National Observatory, USA, ESO La Silla, Chile, Mt. Stromlo Observatory, Australia, Xinglong National Observatory, China, Isaac Newton Telescope, Spain, Laboratório Nacional de Astrofísica, Brazil, and South African Astronomical Observatory, South Africa. Contemporaneous observations from Catania, Italy and Fairborn Observatories, USA, and on data obtained with the Rossi X-ray Timing Explorer.