HMS Illustrious was the first aircraft carrier in the Royal Navy to have an armoured flight deck. All previous designs had wooden decking.
She was used to ferry Spitfires to Malta. During such a convoy called Operation Excess she was badly damaged & had to make for Malta on the 10th January 1941 to undergo emergency repairs. An account of this convoy can be seen by clicking the link in the left column. This was not the safest place to be as the German bomber pilots were instructed to 'sink Illustrious' & consider it a prime target. Being laid up in harbour made her a sitting duck for the bombers & every effort was concentrated on her by the Axis bombers.
On arrival in Grand Harbour she was berthed at Parlatorio Wharf in French Creek. The dead & injured were taken ashore with the wounded being taken to Mtarfa hospital. Work progressed on repairs round the clock. The Engineer Commander said 'Her engines are not too bad, we'll get her away alright'. Maltese workmen were instructed not to repair the flight deck but to concentrate repairs on bare essentials to make the ship seaworthy.

HMS Illustrious under attack July 1941
Photo courtesy of Tony Cox.

The arrival of such an important ship brought a lot of civilian onlookers who crowded the harbour area. At a quarter past noon on the 16th January an announcement was made over loudspeakers to the civilians to make for air raid shelters on hearing the air raid sirens as a new defence strategy was to be used to protect the harbour & flying shrapnel from exploding shellls falling from the sky would make the area very dangerous. Many civilians at this time would stay above ground to watch the bombing.
At 13.55 the radar picked up a large contact - 'It was the largest that had ever been recorded in Malta till then'. The harbour guns lifted to their fixed positions - light AA, heavy AA, 4·5" guns, pom poms, machine guns & even heavy guns on the fort not used as they could not reach high levels were brought to bear against the lower flying dive bombers.
The bombers from Fligerkorps X were escorted by Messerschitt, Fiat & Macchi fighters. The RAF managed to send up 4 Hurricanes, 3 Fulmars & 2 Gladiators. These were instructed to stay out of the harbour area & pick off stragglers. The attack comprised of 2 seperate attacks - the first by Ju 88's (shallow dive bombers) & the second by Ju 87 (Stuka's). This force amounted to 70 bombers all concentrating on sinking Illustrious.
The harbour guns opened up to a deafening noise described as 'hell let loose'. The ships in harbour including Illustrious fired their guns also.
Despite the bravery of the German airmen only one bomb hit Illustrious this being on the quarterdeck & caused little damage.
Despite the RAF pilots being told not to enter the harbour area a Fulmar chased a Stuka right through the barrage. After the bomber released his bombs he swept off down the harbour so low to the water he had to climb to get over the 15' breakwater. The Fulmar eventually shot it down. This returned to Hal Far where the pilot remarked - 'Don't think much of Malta's bloody barrage'. The plane however was so badly damaged it didn't fly again apparently.
During this attack the merchantman Essex was hit by a heavy bomb in the engine room with the loss of 38 men. Luckily the bulkheads contained the explosion. She was loaded with 4,000 tons of ammunition & torpedoes.

The Bombing of HMS Illustrious. This set of 3 photos shows the bombing of HMS Illustrious in Grand Harbour, Malta 1941. The ship can be seen under the crane centre & to the right. I had the first photo in my fathers collection. This was also sent in by Tony Cox. The complete set was kindly sent to me by Keith Bastard. The dockyard floating crane was positioned over the flight deck to prevent low level attacks. See also the Floating Crane page.

Bell of the Illustrious currently in the Malta National War Museum

Senglea Church or what's left of it after it was hit during the attack on HMS Illustrious on 16th January 1941. Photo courtesy of Victor Pulis.

Parlatorio Wharf where Illustrious was brought for repairs. Now it's a huge dry dock area capable of taking super tankers. Taken in 2006.
Illustrious was bombed about where that big yellow crane is standing.

I talked to a Maltese friend in 2006 & was amazed to hear that his father worked in the docks as a ship repairer. He remembers his father talking about working on a ship & that ship suddenly moving without taking the mooring ropes off. These broke off & the labourers were part of the ships company.
Reports also suggest the Illustrious left at great haste the second repairs to make her seaworthy were completed. She did leave without casting off mooring ropes as reports state ropes hanging from Illustrious on exit from harbour. Could this be the same ship?

Written on the back of this photo - HMS Illustrious "going through it" on voyage to Malta January 1941.
Photo courtesy of Michael Longyear

References:
Ernli Bradford Siege Malta 1940 - 1943. Penguin Books.
Malta Convoys. David A. Thomas