We present simultaneous and continuous observations of the H$α$, H$β$, He {\sc i} D$_{3}$, Na {\sc i} D$_{1}$,D$_{2}$ doublet and the Ca {\sc 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 $2\fd8$. Two large optical flares were observed, both showing an increase in the emission of H$α$, Ca {\sc ii} H & K, H$β$ and He {\sc i} D$_{3}$ and a strong filling-in of the Na {\sc i} D$_{1}$,D$_{2}$ 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 H$α$ and He {\sc i} D$_{3}$ 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. Comment: 20 pages, 12 figures, 8 tables, accepted by A&A