I've split it up into sections to which you can jump if you want to:
Go north and enter the door on your right [5]. Click somewhere off your test paper and you'll see the classroom. To find out the correct answers, take a look at the paper of the guy with the big head to your left [10]. The answers are d,e,e,c,e,c,e,d,a,a. When the test is over, go south. Open the second door on the right, which will be what should be a very familiar janitor's closet. The the Scrub-O-Matic [20] and the safety cones [30]. Go south again and take the passage to the right.
Put the cones down on the floor, then put the Scrub-O-Matic on the floor, then open it and use it. Move around and clean all the dirty spots on the floor [80]. Don't take too much time doing it, as it is timed and you'll get into trouble for not getting it finished on time. Watch Quirk make a fool of himself and then go back up the lift and back into the corridor. Go south and have a look at the noticeboard. You'll find that you've passed your test and are to become the captain of a ship [180].
You'll need to leave the chair and the bridge and head back into the engineering section to see what's in the garbage compartment. Open the white garbage compartment door by pressing the blue button to its left, and meet Spike [300]. Use the toolbox in the lower left corner of the screen and take the laser torch [305], spare fuse [310], punch [310] and the antacid tablets [330]. Clean up the toolbox so as not to irk Cliffy. Enter the engineering lab to the left, then exit it and enter it again and walk down a bit and Spike will make an appearance again. Put him in the habitube on the right side of the lab [350], and put in the antacid tablets as well [370].
Go back to the bridge and sit down. Command Droole to lay in a course for Peeyu (92767) and then go to lite speed. When you arrive, go to regular speed and activate RRS [470]. Lay in a course for Kiz Urazgubi (20011). After seeing what happens, go to the science lab, stand on the transporter and talk or command it to beam down [480].
Go back down the the pool where you landed and you'll see WD40 taking off to go and look for you again. Her cloaking device is broken though. Go back to the log screen and crawl half way through the log. When she lands on the log, stick the banana up the tailpipe of her jetpack [815]. Get out of the log and pick up WD40's head that is lying on the ground on the left [840].
Go back down to the pool again, Cliffy will be there and you'll teleport back up to the ship [1015]. Exit the engineering room and then go back into it. Cliffy will give you a remote control device. Beam back down to the planet and you'll appear in a different place. Click the remote control on yourself [1115] and get onto the platform that appears.
Open the panel on the right. Now you have to get the clocking device out in a certain amount of time and get out of there. It goes something like this: Open the top latch, then the bottom latch. Turn all dials, then again. Open the top left panel (by clicking on the little panel next to it), then the bottom right one. Turn the two dials left, then again. Open the top right panel, then the lower left one. Get the cloaking device [1315] and get out of there.
After the salesman leaves, Quirk will challenge you to a game. Beat him without losing any of your ships [1425]. (You get 25 points for each ship that you have left at the end of the game, so you only get all 100 points if all your ships survive.) After Cliffy is taken away, sit at the table again and talk to Flo and Droole. Put the Space Monkeys that the salesman gave you into your drink [1475]. Go to the right and when the security guards leave, use the panel to deactivate the shield [1500] and go to the second cell. Use Spike on the cell's bars [1550] and Cliffy can escape and you teleport back to the ship [1750].
Droole goes off on his own. Go down to the building in the middle (the only one you can enter). Try to use the computer in the middle. You will be attacked and you must dodge the monster's mutating loogies (there will be five of them) [1825]. After the man talks, pick up the piece of paper that he dropped [1830] and look at it. Then use the computer again and type in 80869 and read the entries. Leave the building and go back up to the raised part and then leave to the left and you'll be able to see the can of Primordal Soup. Look at it [1900]. Go back and use your comms device to tell Flo to beam you up then go to the bridge.
Make your way to the pod and look inside it. Take the coat [1980] and press the red button that was underneath it [2015]. Walk left until the ambassador attacks you. You'll both fall over the edge and you'll be hanging on. When you can, give her the coat to hang onto [2050] and she'll climb up. Use your comms device to tell Flo to beam you up [2075] and when the ambassador drops a vine down, grab hold of it [2080].
Go back to the bridge. When you get shot at, tell Droole to take evasive action and go into the asteroid field [2230]. When Cliffy drifts off into space, go to the pod bay. Use the console at the right and press the pod rotation button, then get into the pod. Cliffy is the red dot on your radar display. Head for him and extend the claw. Move towards him until a green box appears on him, then close the claw [2330]. Make your way back to the Eureka [2380].
Head back to the bridge and set a course for the Genetix laboratory - the location was on the can of Primordal Soup on Klorox II (41666). Go to lite speed and when you get there, go to regular speed and then standard orbit [2390]. Beam down to the surface...
Fly onto Cliffy [2600] and then go behind the rock at the right back of the screen. Click on your body [2610] and you will be changed back [2660]. Use the hole punch on the business card [2665] and punch an X shape on the left side of the card. Use the card in the slot [3165] and go inside. Go to the panel at the bottom of the stairs and press the black button to its left, then get the liquid nitrogen [3215]. Go back out the door and tell Cliffy to beam you up.
Tell Cliffy to reverse the polarity of the transporter. Look at the cryo chamber and then put it on 10 seconds defrost [3265]. Open the chamber, then take Beatrice and put her on the transporter [3315]. Chat to WD40 and then go back to the bridge.
When inside, wait for the guard to appear and then leave. Go to the machine in the middle of the room. Use it and replace the distributor cap [3965]. Wait for the guard to come and go again and then go down the gangway and out of the door that the guard came in. Lift up the grating in the middle of the passage and get underneath [4035].
Go north, east, north, north. Now you need to climb up the ladder quickly so as not to get squashed by the elevator. Go up two levels so that you get to level 6. If the lift is in the way, go into the level 7 hatch and then come back and if the elevator has moved then go up to level 6. On level 6, go south, west, north, north, east, north, north. Go up to level 4 and then south, west, north, north, west, west, north, north and then enter the second door hatch from the top. Then go south, south, west, south, east, south [4385]. Use the panel on the wall and turn the shields off [4405].
Get saved by WD40. When in the transporter room, wait until all the Pukoids are on the transporter and then tell Cliffy to activate [4425]. Tell Flo to beam you back to the Eureka [4445]. Go to the bridge and command Droole to fire [4495], then command him to activate RRS [4695]. Command Flo to abandon ship [4705] and then push the red button at your right hand, then the left button on the device [4805].
Go to the engineering room and open the cryochamber [4815]. Get onto the transporter and tell it to energise. Go out of the engineering room and then into the maintenance hatch at the right side of the other end of the passageway. Pull out the fuse in the middle of the row closest to you and replace it with the new one you have [4990]. Go back to the engineering room. When the blob tries to grab you, just go there again and you'll jump in. Get Spike out of the habitube [5000/5000], then get onto the transporter and energise!